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Ghafoori SM, Sethi A, Petersen GF, Tanipour MH, Gooley PR, Forwood JK. RNA Binding Properties of SOX Family Members. Cells 2024; 13:1202. [PMID: 39056784 PMCID: PMC11274882 DOI: 10.3390/cells13141202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
SOX proteins are a family of transcription factors (TFs) that play critical functions in sex determination, neurogenesis, and chondrocyte differentiation, as well as cardiac, vascular, and lymphatic development. There are 20 SOX family members in humans, each sharing a 79-residue L-shaped high mobility group (HMG)-box domain that is responsible for DNA binding. SOX2 was recently shown to interact with long non-coding RNA and large-intergenic non-coding RNA to regulate embryonic stem cell and neuronal differentiation. The RNA binding region was shown to reside within the HMG-box domain; however, the structural details of this binding remain unclear. Here, we show that all SOX family members, except group H, interact with RNA. Our mutational experiments demonstrate that the disordered C-terminal region of the HMG-box domain plays an important role in RNA binding. Further, by determining a high-resolution structure of the HMG-box domain of the group H family member SOX30, we show that despite differences in RNA binding ability, SOX30 shares a very similar secondary structure with other SOX protein HMG-box domains. Together, our study provides insight into the interaction of SOX TFs with RNA.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Ashish Sethi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - Gayle F. Petersen
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Mohammad Hossein Tanipour
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Paul R. Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
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2
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Garg R, DeZonia B, Paterson AL, Rienstra CM. Low power supercycled TPPM decoupling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107726. [PMID: 38991267 DOI: 10.1016/j.jmr.2024.107726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024]
Abstract
Improving the spectral sensitivity and resolution of biological solids is one of the long-standing problems in nuclear magnetic resonance (NMR) spectroscopy. In this report, we introduce low-power supercycled variants of two-pulse phase-modulated (TPPM) sequence for heteronuclear decoupling. The utility of the sequence is shown by improvements in the transverse relaxation time of observed nuclei (with 1H decoupling) with its application to different samples (uniformly 13C, 15N, 2H-labeled GB1 back-exchanged with 25% H2O and 75% D2O, uniformly 13C, 15N, 2H-labeled human derived Asyn fibril back-exchanged with 100% H2O and uniformly 13C, 15N -labeled human derived Asyn fibril) at fast MAS using low radiofrequency (RF) fields. To understand the effect of spinning speed, the transverse relaxation time is monitored under different spinning frequencies. In comparison to existing heteronuclear decoupling sequences, the supercycled TPPM (sTPPM) sequence significantly improves the spectral sensitivity and resolution and is robust towards B1 inhomogeneity and decoupler offset.
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Affiliation(s)
- Rajat Garg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States.
| | - Barry DeZonia
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, United States.
| | - Alexander L Paterson
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, United States.
| | - Chad M Rienstra
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, United States; Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, United States.
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3
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İncir İ, Kaplan Ö. Escherichia coli as a versatile cell factory: Advances and challenges in recombinant protein production. Protein Expr Purif 2024; 219:106463. [PMID: 38479588 DOI: 10.1016/j.pep.2024.106463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 05/08/2024]
Abstract
E. coli plays a substantial role in recombinant protein production. Its importance increased with the discovery of recombinant DNA technology and the subsequent production of the first recombinant insulin in E. coli. E. coli is a widely used and cost-effective host to produce recombinant proteins. It is also noteworthy that a significant portion of the approved therapeutic proteins have been produced in this organism. Despite these advantages, it has some disadvantages, such as toxicity and lack of eukaryotic post-translational modifications that can lead to the production of misfolded, insoluble, or dysfunctional proteins. This study focused on the challenges and engineering approaches for improved expression and solubility in recombinant protein production in E. coli. In this context, solution strategies such as strain and vector selection, codon usage, mRNA stability, expression conditions, translocation to the periplasmic region and addition of fusion tags in E. coli were discussed.
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Affiliation(s)
- İbrahim İncir
- Karamanoğlu Mehmetbey University, Kazım Karabekir Vocational School, Department of Medical Services and Techniques, Environmental Health Program Karaman, Turkey.
| | - Özlem Kaplan
- Alanya Alaaddin Keykubat University, Rafet Kayış Faculty of Engineering, Department of Genetics and Bioengineering, Antalya, Turkey.
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4
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Sword TT, Dinglasan JLN, Abbas GSK, Barker JW, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system. Sci Rep 2024; 14:12983. [PMID: 38839808 PMCID: PMC11153635 DOI: 10.1038/s41598-024-61376-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Ghaeath S K Abbas
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
- School of Chemistry, University of Sydney, Sydney, NSW, Australia
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Madeline E Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Elijah R Greene
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Damian S Gooden
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Scott J Emrich
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Michael A Gilchrist
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
- School of Chemistry, University of Sydney, Sydney, NSW, Australia.
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5
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Li S, Ye Z, Moreb EA, Menacho-Melgar R, Golovsky M, Lynch MD. 2-Stage microfermentations. Metab Eng Commun 2024; 18:e00233. [PMID: 38665924 PMCID: PMC11043886 DOI: 10.1016/j.mec.2024.e00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Cell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of protocols for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, by detailing the approach to protocol development, these methods are also adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.
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Affiliation(s)
- Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A. Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Michael D. Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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6
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Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AI, Ackermann BE, Hui T, Lin YS, Debelouchina GT, Shoulders MD. The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure. SCIENCE ADVANCES 2024; 10:eadl6144. [PMID: 38640233 PMCID: PMC11029814 DOI: 10.1126/sciadv.adl6144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yu Meng Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cheenou Her
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Robert A. Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Hui
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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7
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Read BJ, Mitchell JBO, da Silva RG. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release. Commun Chem 2024; 7:77. [PMID: 38582930 PMCID: PMC10998830 DOI: 10.1038/s42004-024-01165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.
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Affiliation(s)
- Benjamin J Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - John B O Mitchell
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.
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8
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Berthold DA, Gordon IR, Liu J, Milchberg MH, O'Shea JY, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Perrin RJ, Perlmutter JS, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat Commun 2024; 15:2750. [PMID: 38553463 PMCID: PMC10980826 DOI: 10.1038/s41467-024-46832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Collin G Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine Basore
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Deborah A Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Isabelle R Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Moses H Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jennifer Y O'Shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brock Summers
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Owen A Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard J Perrin
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joel S Perlmutter
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Radiology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Paul T Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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9
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Fristot E, Cambray G, Bonnet J. LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri. ACS Synth Biol 2024; 13:951-957. [PMID: 38335132 DOI: 10.1021/acssynbio.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Lactic acid bacteria (LAB) are important for many biotechnological applications such as bioproduction and engineered probiotics for therapy. Inducible promoters are key gene expression control elements, yet those available in LAB are mainly based on bacteriocin systems and have many drawbacks, including large gene clusters, costly inducer peptides, and little portability to in vivo settings. Using Lactobacillus gasseri, a model commensal bacteria from the human gut, we report the engineering of synthetic LactoSpanks promoters (Pls), a collection of variable strength inducible promoters controlled by the LacI repressor from E. coli and induced by isopropyl β-d-1-thiogalactopyranoside (IPTG). We first show that the Phyper-spank promoter from Bacillus subtilis is functional in L. gasseri, albeit with substantial leakage. We then construct and screen a semirational library of Phyper-spank variants to select a set of four IPTG-inducible promoters that span a range of expression levels and exhibit reduced leakages and operational dynamic ranges (from ca. 9 to 28 fold-change). With their low genetic footprint and simplicity of use, LactoSpanks will support many applications in L. gasseri, and potentially other lactic acid and Gram-positive bacteria.
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Affiliation(s)
- Elsa Fristot
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), University of Montpellier, INRAE UMR1333, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
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10
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Alanis E, Aguilar F, Banaei N, Dean FB, Villarreal A, Alanis M, Lozano K, Bullard JM, Zhang Y. A rationally designed antimicrobial peptide from structural and functional insights of Clostridioides difficile translation initiation factor 1. Microbiol Spectr 2024; 12:e0277323. [PMID: 38329351 PMCID: PMC10913371 DOI: 10.1128/spectrum.02773-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
A significant increase of hospital-acquired bacterial infections during the COVID-19 pandemic has become an urgent medical problem. Clostridioides difficile is an urgent antibiotic-resistant bacterial pathogen and a leading causative agent of nosocomial infections. The increasing recurrence of C. difficile infection and antibiotic resistance in C. difficile has led to an unmet need for the discovery of new compounds distinctly different from present antimicrobials, while antimicrobial peptides as promising alternatives to conventional antibiotics have attracted growing interest recently. Protein synthesis is an essential metabolic process in all bacteria and a validated antibiotic target. Initiation factor 1 from C. difficile (Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here, we report the solution nuclear magnetic resonance (NMR) structure of Cd-IF1 which adopts a typical β-barrel fold and consists of a five-stranded β-sheet and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. The interaction of Cd-IF1 with the 30S ribosomal subunit was studied by NMR titration for the construction of a structural model of Cd-IF1 binding with the 30S subunit. The short α-helix in IF1 was found to be critical for IF1 ribosomal binding. A peptide derived from this α-helix was tested and displayed a high ability to inhibit the growth of C. difficile and other bacterial strains. These results provide a clue for the rational design of new antimicrobials.IMPORTANCEBacterial infections continue to represent a major worldwide health hazard due to the emergence of drug-resistant strains. Clostridioides difficile is a common nosocomial pathogen and the causative agent in many infections resulting in an increase in morbidity and mortality. Bacterial protein synthesis is an essential metabolic process and an important target for antibiotic development; however, the precise structural mechanism underlying the process in C. difficile remains unknown. This study reports the solution structure of C. difficile translation initiation factor 1 (IF1) and its interaction with the 30S ribosomal subunit. A short α-helix in IF1 structure was identified as critically important for ribosomal binding and function in regulating the translation initiation, which allowed a rational design of a new peptide. The peptide demonstrated a high ability to inhibit bacterial growth with broad-spectrum antibacterial activity. This study provides a new clue for the rational design of new antimicrobials against bacterial infections.
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Affiliation(s)
- Elvira Alanis
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Faith Aguilar
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Frank B. Dean
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Alexa Villarreal
- Department of Mechanical Engineering, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Miguel Alanis
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Karen Lozano
- Department of Mechanical Engineering, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - James M. Bullard
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Yonghong Zhang
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, Texas, USA
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11
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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12
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Wen F, Wang Y, Tu B, Cui L. Superfast Gelation of Spider Silk-Based Artificial Silk Protein. Gels 2024; 10:69. [PMID: 38247791 PMCID: PMC10815891 DOI: 10.3390/gels10010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Spider silk proteins (spidroins) have garnered attention in biomaterials research due to their ability to self-assemble into hydrogels. However, reported spidroin hydrogels require high protein concentration and prolonged gelation time. Our study engineered an artificial spidroin that exhibits unprecedented rapid self-assembly into hydrogels at physiologically relevant conditions, achieving gelation at a low concentration of 6 mg/mL at 37 °C without external additives. Remarkably, at a 30 mg/mL concentration, our engineered protein forms hydrogels within 30 s, a feature we termed "superfast gelation". This rapid formation is modulated by ions, pH, and temperature, offering versatility in biomedical applications. The hydrogel's capacity to encapsulate proteins and support E. coli growth while inducing RFP expression provides a novel platform for drug delivery and bioengineering applications. Our findings introduce a superfast, highly adaptable, and cytocompatible hydrogel that self-assembles under mild conditions, underscoring the practical implication of rapid gelation in biomedical research and clinical applications.
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Affiliation(s)
- Fan Wen
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
| | - Yu Wang
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
| | - Bowen Tu
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou 213000, China;
| | - Lun Cui
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
- Biomaterials Lab, Changzhou AiRiBio Healthcare Co., Ltd., Changzhou 213164, China
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13
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He S, Taher NM, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR. Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.572601. [PMID: 38293063 PMCID: PMC10827105 DOI: 10.1101/2024.01.16.572601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa infects cystic fibrosis (CF) patient airways and produces a virulence factor Cif that is associated with worse outcomes. Cif is an epoxide hydrolase that reduces cell-surface abundance of the cystic fibrosis transmembrane conductance regulator (CFTR) and sabotages pro-resolving signals. Its expression is regulated by a divergently transcribed TetR family transcriptional repressor. CifR represents the first reported epoxide-sensing bacterial transcriptional regulator, but neither its interaction with cognate operator sequences nor the mechanism of activation has been investigated. Using biochemical and structural approaches, we uncovered the molecular mechanisms controlling this complex virulence operon. We present here the first molecular structures of CifR alone and in complex with operator DNA, resolved in a single crystal lattice. Significant conformational changes between these two structures suggest how CifR regulates the expression of the virulence gene cif. Interactions between the N-terminal extension of CifR with the DNA minor groove of the operator play a significant role in the operator recognition of CifR. We also determined that cysteine residue Cys107 is critical for epoxide sensing and DNA release. These results offer new insights into the stereochemical regulation of an epoxide-based virulence circuit in a critically important clinical pathogen.
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Affiliation(s)
- Susu He
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Noor M. Taher
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Kelli L. Hvorecny
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Michael J. Ragusa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
- Department of Chemistry, Dartmouth, Hanover, NH 03755 USA
| | - Christopher D. Bahl
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Alison B. Hickman
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Fred Dyda
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Dean R. Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
- Department of Chemistry, Dartmouth, Hanover, NH 03755 USA
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14
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Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
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Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
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15
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Thakkar H, Chatterjee S, Saxena P, Eerla R, Wagh S, Khairnar A, Shah RP. Cell-Engineered Recombinant α-Synuclein: A Gage R&R Validated Protocol. J Proteome Res 2024; 23:16-24. [PMID: 37985371 DOI: 10.1021/acs.jproteome.3c00190] [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: 11/22/2023]
Abstract
α-Synuclein (α-Syn) misfolding and its presence in Lewy bodies are observed in almost all Parkinson's disease (PD) patients. Basic biomedical research would benefit from a quick, low-cost approach to purifying α-Syn and developing in vitro and in vivo models for PD. Several research groups utilize PFF-based models, yet the production of α-Syn PFFs is inconsistent, resulting in nonconclusive findings. Some research laboratories prepare recombinant α-Syn (r α-Syn) by molecular cloning to overexpress α-Syn with various purifying techniques. Laboratory-to-laboratory protocols cause considerable variability and sometimes contradictory findings. PD researchers spend more on protein than solving α-Syn's riddles. This article uncovered a novel method for expressing and purifying r α-Syn validated through gage reproducibility and repeatability (Gage R&R). For the production of r α-Syn, we have employed the ability of a high-cell-density-based expression system to overexpress protein in BL21(DE3). A simple, high-throughput, nonchromatographical purification protocol has been devised to facilitate research with higher reproducibility, which was validated through Gage R&R. A crossover experimental design was utilized, and the purified protein was characterized using orthogonal high-end analytical methods, which displayed higher similarity between the isolated r α-Syn. Batch-to-batch variability was the least for produced protein and hence can be utilized for exploring the iceberg of PD.
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Affiliation(s)
- Harsh Thakkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Sayan Chatterjee
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Purvi Saxena
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Rameswari Eerla
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Sachin Wagh
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Amit Khairnar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
| | - Ravi P Shah
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research─Ahmedabad (NIPER-A), Opposite Air force Station Palaj, Gandhinagar 382355, Gujarat India
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16
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Sun M, Gao AX, Li A, Ledesma-Amaro R, Wang P, Chen W, Bai Z, Liu X. Hyper-production of porcine contagious pleuropneumonia subunit vaccine proteins in Escherichia coli by developing a bicistronic T7 expression system. Biotechnol J 2024; 19:e2300187. [PMID: 38178735 DOI: 10.1002/biot.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
The ApxII toxin and the outer membrane lipoprotein (Oml) of Actinobacillus pleuropneumoniae are important vaccine antigens against porcine contagious pleuropneumonia (PCP), a prevalent infectious disease affecting the swine industry worldwide. Previous studies have reported the recombinant expression of ApxII and Oml in Escherichia coli; however, their yields were not satisfactory. Here, we aimed to enhance the production of ApxII and Oml by constructing a bicistronic expression system based on the widely used T7 promoter. To create efficient T7 bicistronic expression cassettes, 16 different fore-cistron sequences were introduced downstream of the T7 promoter. The expression of three vaccine antigens Oml1, Oml7, and ApxII in the four strongest bicistronic vectors were enhanced compared to the monocistronic control. Further optimization of the fermentation conditions in micro-well plates (MWP) led to improved production. Finally, the production yields reached unprecedented levels of 2.43 g L-1 of Oml1, 2.59 g L-1 of Oml7, and 1.21 g L-1 of ApxII, in a 5 L bioreactor. These three antigens also demonstrated well-protective immunity against A. pleuropneumoniae infection. In conclusion, this study establishes an efficient bicistronic T7 expression system that can be used to express recombinant proteins in E. coli and achieves the hyper-production of PCP vaccine proteins.
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Affiliation(s)
- Manman Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - An Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Peng Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Wenchao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
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17
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Sword TT, Dinglasan JLN, Abbas GS, William Barker J, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569483. [PMID: 38077034 PMCID: PMC10705458 DOI: 10.1101/2023.11.30.569483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T. Sword
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Jaime Lorenzo N. Dinglasan
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Ghaeath S.K. Abbas
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
| | - J. William Barker
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Madeline E. Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Elijah R. Greene
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Damian S. Gooden
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Scott J. Emrich
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Michael A. Gilchrist
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
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18
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Treviño MÁ, Pantoja-Uceda D, Laurents DV, Mompeán M. SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA. Nucleic Acids Res 2023; 51:10041-10048. [PMID: 37665006 PMCID: PMC10570013 DOI: 10.1093/nar/gkad714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
The SARS-CoV-2 Nsp8 protein is a critical component of the RNA replicase, as its N-terminal domain (NTD) anchors Nsp12, the RNA, and Nsp13. Whereas its C-terminal domain (CTD) structure is well resolved, there is an open debate regarding the conformation adopted by the NTD as it is predicted as disordered but found in a variety of complex-dependent conformations or missing from many other structures. Using NMR spectroscopy, we show that the SARS CoV-2 Nsp8 NTD features both well folded secondary structure and disordered segments. Our results suggest that while part of this domain corresponding to two long α-helices forms autonomously, the folding of other segments would require interaction with other replicase components. When isolated, the α-helix population progressively declines towards the C-termini but surprisingly binds dsRNA while preserving structural disorder.
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Affiliation(s)
- Miguel Á Treviño
- “Blas Cabrera” Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain
| | - David Pantoja-Uceda
- “Blas Cabrera” Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain
| | - Douglas V Laurents
- “Blas Cabrera” Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain
| | - Miguel Mompeán
- “Blas Cabrera” Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, Madrid 28006, Spain
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19
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Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AM, Ackermann BE, Debelouchina GT, Shoulders MD. The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556894. [PMID: 37745335 PMCID: PMC10515774 DOI: 10.1101/2023.09.08.556894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 °C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape. Teaser Pro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.
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20
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Medha, Priyanka, Sharma S, Sharma M. PE_PGRS45 (Rv2615c) protein of Mycobacterium tuberculosis perturbs mitochondria of macrophages. Immunol Cell Biol 2023. [PMID: 37565603 DOI: 10.1111/imcb.12677] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
The PE_PGRS proteins have coevolved with the antigenic ESX-V secretory system and are abundant in pathogenic Mycobacterium. Only a few PE_PGRS proteins have been characterized, and research suggests their role in organelle targeting, cell death pathways, calcium (Ca2+ ) homeostasis and disease pathogenesis. The PE_PGRS45 (Rv2615c) protein was predicted to contain mitochondria targeting sequences by in silico evaluation. Therefore, we investigated the targeting of the Rv2615c protein to host mitochondria and its effect on mitochondrial functions. In vitro experiments showed the Rv2615c protein colocalized with the mitochondria and led to morphological mitochondrial perturbations. Recombinant Rv2615c was observed to cause increased levels of intracellular reactive oxygen species and the adenosine diphosphate-to-adenosine triphosphate ratio. The Rv2615c protein also induced mitochondrial membrane depolarization and the generation of mitochondrial superoxide. We observed the release of cytochrome C into the cytoplasm and increased expression of proapoptotic genes Bax and Bim with no significant change in anti-apoptotic Bcl2 in Rv2615c-stimulated THP1 macrophages. Ca2+ is a key signaling molecule in tuberculosis pathogenesis, modulating host cell responses. As reported for other PE_PGRS proteins, Rv2615c also has Ca2+ -binding motifs and thus can modulate calcium homeostasis in the host. We also observed a high level of Ca2+ influx in THP1 macrophages stimulated with Rv2615c. Based on these findings, we suggest that Rv2615c may be an effector protein that could contribute to disease pathogenesis by targeting host mitochondria.
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Affiliation(s)
- Medha
- DSKC BioDiscovery Laboratory, Department of Zoology, Miranda House, University of Delhi, Delhi, India
| | - Priyanka
- DSKC BioDiscovery Laboratory, Department of Zoology, Miranda House, University of Delhi, Delhi, India
| | - Sadhna Sharma
- DSKC BioDiscovery Laboratory, Department of Zoology, Miranda House, University of Delhi, Delhi, India
| | - Monika Sharma
- DSKC BioDiscovery Laboratory, Department of Zoology, Miranda House, University of Delhi, Delhi, India
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21
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Figiel M, Szubert F, Luchinat E, Bonarek P, Baranowska A, Wajda-Nikiel K, Wilamowski M, Miłek P, Dziedzicka-Wasylewska M, Banci L, Górecki A. Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194905. [PMID: 36581245 DOI: 10.1016/j.bbagrm.2022.194905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022]
Abstract
Human protein Yin Yang 1 (YY1) controls the transcription of hundreds of genes both positively and negatively through interactions with a wide range of partner proteins. Results presented here from proteolytic sensitivity, calorimetry, circular dichroism, fluorescence, NMR, size-exclusion chromatography, SELEX, and EMSA show that purified YY1 forms dimers via its disordered N-terminal region with strong zinc-ion concentration dependence. The YY1 dimer is shown to bind tandem repeats of a canonical recognition DNA sequence with high affinity, and analysis of human YY1 regulatory sites shows that many contain repeats of its recognition elements. YY1 dimerization may compete with partner protein interactions, making control by zinc ion concentration a previously unrecognized factor affecting YY1 gene regulation. Indeed, YY1 is known to be important in many pathogenic processes, including neoplasia, in which zinc ion concentrations are altered. The present results incentivize studies in vivo or in vitro that explore the role of zinc ion concentration in YY1-mediated gene expression.
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Affiliation(s)
- Małgorzata Figiel
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Filip Szubert
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine - CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Baranowska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Katarzyna Wajda-Nikiel
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Mateusz Wilamowski
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Piotr Miłek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019, Florence, Italy
| | - Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
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22
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Dregni AJ, McKay MJ, Surya W, Queralt-Martin M, Medeiros-Silva J, Wang HK, Aguilella V, Torres J, Hong M. The Cytoplasmic Domain of the SARS-CoV-2 Envelope Protein Assembles into a β-Sheet Bundle in Lipid Bilayers. J Mol Biol 2023; 435:167966. [PMID: 36682677 PMCID: PMC9851921 DOI: 10.1016/j.jmb.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein forms a pentameric ion channel in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of the infected cell. The cytoplasmic domain of E interacts with host proteins to cause virus pathogenicity and may also mediate virus assembly and budding. To understand the structural basis of these functions, here we investigate the conformation and dynamics of an E protein construct (residues 8-65) that encompasses the transmembrane domain and the majority of the cytoplasmic domain using solid-state NMR. 13C and 15N chemical shifts indicate that the cytoplasmic domain adopts a β-sheet-rich conformation that contains three β-strands separated by turns. The five subunits associate into an umbrella-shaped bundle that is attached to the transmembrane helices by a disordered loop. Water-edited NMR spectra indicate that the third β-strand at the C terminus of the protein is well hydrated, indicating that it is at the surface of the β-bundle. The structure of the cytoplasmic domain cannot be uniquely determined from the inter-residue correlations obtained here due to ambiguities in distinguishing intermolecular and intramolecular contacts for a compact pentameric assembly of this small domain. Instead, we present four structural topologies that are consistent with the measured inter-residue contacts. These data indicate that the cytoplasmic domain of the SARS-CoV-2 E protein has a strong propensity to adopt β-sheet conformations when the protein is present at high concentrations in lipid bilayers. The equilibrium between the β-strand conformation and the previously reported α-helical conformation may underlie the multiple functions of E in the host cell and in the virion.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Maria Queralt-Martin
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Vicente Aguilella
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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23
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de Divitiis M, Ami D, Pessina A, Palmioli A, Sciandrone B, Airoldi C, Regonesi ME, Brambilla L, Lotti M, Natalello A, Brocca S, Mangiagalli M. Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:30. [PMID: 36823649 PMCID: PMC9948444 DOI: 10.1186/s13068-023-02281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose. RESULTS The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness. CONCLUSIONS CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
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Affiliation(s)
- Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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24
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Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, Moritz RL. Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline. J Proteome Res 2023; 22:647-655. [PMID: 36629399 PMCID: PMC10234491 DOI: 10.1021/acs.jproteome.2c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform.
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Affiliation(s)
| | | | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
| | - Andrew S. Lyon
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA 94143
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA 94143
| | - Qing Luan
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA 97403
| | - Brad J. Nolen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA 97403
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA 98195
| | - Trisha N. Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
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25
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In Vitro Pharmacokinetics of LL-37 and Oncorhyncin II Combination Against Acinetobacter baumannii. Jundishapur J Microbiol 2023. [DOI: 10.5812/jjm-131299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Multidrug-resistant (MDR) Acinetobacter baumannii is one of the most common nosocomial pathogens. Antimicrobial peptides (AMPs) have been introduced as a viable alternative to antibiotics in the treatment of MDR pathogens. Objectives: This study was designed to assess the in vitro pharmacokinetics of the combination of two potent AMPs, LL-37 and oncorhyncin II, against A. baumannii (ATCC19606). Methods: The synthesized genes of oncorhyncin II and LL-37 were introduced into Escherichia coli BL21 as the expression host. The minimum inhibitory concentration (MIC), time-kills, and growth kinetics of these peptides were used to evaluate their antimicrobial efficiencies against A. baumannii (ATCC19606). Results: LL-37 and oncorhyncin II recombinant peptides showed MIC of 30.6 and 95.87 µg/mL against A. baumannii, respectively. Additive action was confirmed by combining the generated AMPs at the checkerboard approach. The combination of LL-37 and oncorhyncin II at 2 × MIC resulted in a rapid drop in log10 CFU/mL of A. baumannii in the time-kill and growth kinetic findings studies. Conclusions: The combination of the produced LL-37 and oncorhyncin II synergizes the bioactivity of the individual peptides. Therefore, these peptides or their combinations might function as novel antibiotics and be used to develop and produce new antimicrobial drugs for the treatment of infections caused by A. baumannii.
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26
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Gordon IR, Liu J, Milchberg MH, O’shea J, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523303. [PMID: 36711931 PMCID: PMC9882085 DOI: 10.1101/2023.01.09.523303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21 helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D. Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander M. Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin G. Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Isabelle R. Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Moses H. Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer O’shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J. Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Owen A. Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - James A. J. Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles D. Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706 USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul T. Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
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27
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Lopez JM. Combined H-N Cross-Polarization and Carbonyl Detection NMR Spectroscopy Allow to Record High-Resolution, High-Sensitivity Spectra of Alpha-Synuclein in Bacterial Cells. Methods Mol Biol 2023; 2551:449-460. [PMID: 36310219 DOI: 10.1007/978-1-0716-2597-2_28] [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: 06/16/2023]
Abstract
Studies of intrinsically disordered proteins (IDPs) under physiological conditions by conventional NMR methods based on proton detection are severely limited by fast proton amide solvent exchange. Carbon detection has been proposed as a solution to the exchange problem but is hampered by low sensitivity. Here, we present a protocol combining proton-nitrogen cross-polarization and carbonyl detection to record high-resolution and high-sensitivity NMR spectra of IDPs under physiological conditions. The protocol describes a step-by-step method to register high-quality N-CO correlation spectrum of alpha-synuclein in E.coli bacterial cells at 37 °C.
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Affiliation(s)
- Juan M Lopez
- Pontificia Universidad Católica del Perú, Departamento de Ciencias - Química, CERMN, Lima, Perú.
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28
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Lee HD, Yoo SK, Yoo HS, Yun CH, Kim GJ. Expression and Characterization of Monomeric Recombinant Isocitrate Dehydrogenases from Corynebacterium glutamicum and Azotobacter vinelandii for NADPH Regeneration. Int J Mol Sci 2022; 23:ijms232315318. [PMID: 36499645 PMCID: PMC9736777 DOI: 10.3390/ijms232315318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The enzymatic transformation of various chemicals, especially using NADPH-dependent hydroxylase, into more soluble and/or high value-added products has steadily garnered increasing attention. However, the industrial application of these NADPH-dependent hydroxylases has been limited due to the high cost of the cofactor NADPH. As an alternative, enzymatic NADPH-regeneration systems have been developed and are frequently used in various fields. Here, we expressed and compared two recombinant isocitrate dehydrogenases (IDHs) from Corynebacterium glutamicum and Azotobacter vinelandii in Escherichia coli. Both enzymes were hyper-expressed in the soluble fraction of E. coli and were single-step purified to apparent homogeneity with yields of more than 850 mg/L. These enzymes also functioned well when paired with NADPH consumption systems. Specifically, NADPH was regenerated from NADP+ when an NADPH-consuming cytochrome P450 BM3 from Bacillus megaterium was incorporated. Therefore, both enzymes could be used as alternatives to the commonly used regeneration system for NADPH. These enzymes also have promising potential as genetic fusion partners with NADPH-dependent enzymes due to the monomeric nature of their quaternary structure, thereby resulting in self-sufficient biocatalysts via NADPH regeneration in a single polypeptide with NADPH-dependent activity.
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Affiliation(s)
- Hun-Dong Lee
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Su-Kyoung Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Ho-Seok Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
- Correspondence: ; Tel.: +82-62-530-3403; Fax: +82-62-530-3409
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29
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Labat-de-Hoz L, Comas L, Rubio-Ramos A, Casares-Arias J, Fernández-Martín L, Pantoja-Uceda D, Martín MT, Kremer L, Jiménez MA, Correas I, Alonso MA. Structure and function of the N-terminal extension of the formin INF2. Cell Mol Life Sci 2022; 79:571. [PMID: 36306014 PMCID: PMC9616786 DOI: 10.1007/s00018-022-04581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
In INF2—a formin linked to inherited renal and neurological disease in humans—the DID is preceded by a short N-terminal extension of unknown structure and function. INF2 activation is achieved by Ca2+-dependent association of calmodulin (CaM). Here, we show that the N-terminal extension of INF2 is organized into two α-helices, the first of which is necessary to maintain the perinuclear F-actin ring and normal cytosolic F-actin content. Biochemical assays indicated that this helix interacts directly with CaM and contains the sole CaM-binding site (CaMBS) detected in INF2. The residues W11, L14 and L18 of INF2, arranged as a 1-4-8 motif, were identified as the most important residues for the binding, W11 being the most critical of the three. This motif is conserved in vertebrate INF2 and in the human population. NMR and biochemical analyses revealed that CaM interacts directly through its C-terminal lobe with the INF2 CaMBS. Unlike control cells, INF2 KO cells lacked the perinuclear F-actin ring, had little cytosolic F-actin content, did not respond to increased Ca2+ concentrations by making more F-actin, and maintained the transcriptional cofactor MRTF predominantly in the cytoplasm. Whereas expression of intact INF2 restored all these defects, INF2 with inactivated CaMBS did not. Our study reveals the structure of the N-terminal extension, its interaction with Ca2+/CaM, and its function in INF2 activation.
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Affiliation(s)
- Leticia Labat-de-Hoz
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Laura Comas
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Armando Rubio-Ramos
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Javier Casares-Arias
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Laura Fernández-Martín
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - David Pantoja-Uceda
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - M Teresa Martín
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Leonor Kremer
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - M Angeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Department of Molecular Biology, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular (CBM) Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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Vesely CH, Reardon PN, Yu Z, Barbar E, Mehl RA, Cooley RB. Accessing isotopically labeled proteins containing genetically encoded phosphoserine for NMR with optimized expression conditions. J Biol Chem 2022; 298:102613. [PMID: 36265582 PMCID: PMC9678770 DOI: 10.1016/j.jbc.2022.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Phosphoserine (pSer) sites are primarily located within disordered protein regions, making it difficult to experimentally ascertain their effects on protein structure and function. Therefore, the production of 15N- (and 13C)-labeled proteins with site-specifically encoded pSer for NMR studies is essential to uncover molecular mechanisms of protein regulation by phosphorylation. While genetic code expansion technologies for the translational installation of pSer in Escherichia coli are well established and offer a powerful strategy to produce site-specifically phosphorylated proteins, methodologies to adapt them to minimal or isotope-enriched media have not been described. This shortcoming exists because pSer genetic code expansion expression hosts require the genomic ΔserB mutation, which increases pSer bioavailability but also imposes serine auxotrophy, preventing growth in minimal media used for isotopic labeling of recombinant proteins. Here, by testing different media supplements, we restored normal BL21(DE3) ΔserB growth in labeling media but subsequently observed an increase of phosphatase activity and mis-incorporation not typically seen in standard rich media. After rounds of optimization and adaption of a high-density culture protocol, we were able to obtain ≥10 mg/L homogenously labeled, phosphorylated superfolder GFP. To demonstrate the utility of this method, we also produced the intrinsically disordered serine/arginine-rich region of the SARS-CoV-2 Nucleocapsid protein labeled with 15N and pSer at the key site S188 and observed the resulting peak shift due to phosphorylation by 2D and 3D heteronuclear single quantum correlation analyses. We propose this cost-effective methodology will pave the way for more routine access to pSer-enriched proteins for 2D and 3D NMR analyses.
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Affiliation(s)
- Cat Hoang Vesely
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Ryan A. Mehl
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Richard B. Cooley
- GCE4All Research Center, Oregon State University, Corvallis, Oregon, USA,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA,For correspondence: Richard B. Cooley
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Shariati FS, Keramati M, Cohan RA. Indirect optimization of staphylokinase expression level in dicistronic auto-inducible system. AMB Express 2022; 12:124. [PMID: 36138332 PMCID: PMC9500143 DOI: 10.1186/s13568-022-01464-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Design of experiment (DOE) is a statistical approach for designing, performing, and interpreting a large set of data with the minimum number of tests. In our previous study, we developed a novel Hsp27 SILEX system for production of recombinant proteins. In the present study, we optimized indirectly the most effective factors including inoculation load, self-induction temperature, and culture media on autoinduction of staphylokinase (SAK) expression using RSM methodology and fluorometry. The expression level of SAK was assayed at different runs after 6 h incubation at 90 rpm. The results indicated all parameters significantly affect the SAK expression level (p < 0.05). The optimum expression condition was obtained with an inoculation load of 0.05, a temperature of 25 °C, and TB culture medium. The analysis of variance with a R2 value of 0.91 showed that a quadratic model well described this prediction (p < 0.05). Applying the optimized condition led to an approximately fourfold increase in the SAK expression level (from 1.3 to 5.2 µg/ml). Moreover, the recombinant protein was purified using immobilized metal affinity chromatography and the activity was also confirmed by semi-quantitative caseinolytic method.
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Affiliation(s)
- Fatemeh Sadat Shariati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Malihe Keramati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
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Enfuvirtide biosynthesis in thermostable chaperone-based fusion. BIOTECHNOLOGY REPORTS 2022; 35:e00734. [PMID: 35646620 PMCID: PMC9130503 DOI: 10.1016/j.btre.2022.e00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022]
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Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes. Sci Rep 2022; 12:11231. [PMID: 35789157 PMCID: PMC9253027 DOI: 10.1038/s41598-022-13561-y] [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: 03/29/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
Structures of protein–ligand complexes provide critical information for drug design. Most protein–ligand complex structures are determined using X-ray crystallography, but where crystallography is not able to generate a structure for a complex, NMR is often the best alternative. However, the available tools to enable rapid and robust structure determination of protein–ligand complexes by NMR are currently limited. This leads to situations where projects are either discontinued or pursued without structural data, rendering the task more difficult. We previously reported the NMR Molecular Replacement (NMR2) approach that allows the structure of a protein–ligand complex to be determined without requiring the cumbersome task of protein resonance assignment. Herein, we describe the NMR2 approach to determine the binding pose of a small molecule in a weak protein–ligand complex by collecting sparse protein methyl-to-ligand NOEs from a selectively labeled protein sample and an unlabeled ligand. In the selective labeling scheme all methyl containing residues of the protein are protonated in an otherwise deuterated background. This allows measurement of intermolecular NOEs with greater sensitivity using standard NOESY pulse sequences instead of isotope-filtered NMR experiments. This labelling approach is well suited to the NMR2 approach and extends its utility to include larger protein–ligand complexes.
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Ayoub Meigouni M, Abouie Mehrizi A, Fazaeli A, Zakeri S, Djadid ND. Optimization of the heterologous expression and purification of Plasmodium falciparum generative cell specific 1 in Escherichia coli. Protein Expr Purif 2022; 198:106126. [PMID: 35661702 DOI: 10.1016/j.pep.2022.106126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/17/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
Abstract
Generative cell specific 1 (GCS1) or Hapless2 (Hap2) is a main transmission-blocking vaccine (TBV) candidate against malaria. Experience has shown that this protein is difficult to express in heterologous hosts. In a study, Plasmodium falciparum GCS1 (PfGCS1) could be expressed in fusion with Glutathione S Transferase (GST). Since the large fusions could influence the immunogenicity of the recombinant antigens, in the current study we tried to express PfGCS1 protein without large fusion tags with an appropriate yield and purity in E. coli. To this end, pfgcs1 gene was codon-optimized and cloned in pET23a plasmid. The expression was evaluated in different E. coli hosts [E. coli BL21(DE3), E. coli BL21(DE3) pLysS, E. coli Rosetta(DE3), and E. coli Rosettagami(DE3)] and media cultures. In addition, the effect of post-induction times, inducer concentration, temperature, and supplementation of glucose and ethanol to culture media were evaluated. The obtained results revealed that rPfGCS1 protein was expressed in all examined E. coli hosts and media cultures with different yields, with the best yield in E. coli BL21(DE3), and E. coli Rosetta(DE3) hosts in TB medium, 16 h post-induction. The expression of rPfGCS1 was confirmed by western blotting using anti-His antibodies. Expression in low temperature at 20 °C and addition of glucose and ethanol to TB media could improve the expression of rPfGCS1. We could express and purify rPfGCS1 without a large fusion protein with an appropriate yield and purity in E. coli Rosetta(DE3). We will evaluate this antigen as TBV candidate against P. falciparum transmission in the future.
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Affiliation(s)
- Masoumeh Ayoub Meigouni
- , Malaria and Vector Research Group, Biotechnology Research Group, Pasteur Institute of Iran, Tehran, Iran; , Department of Parasitology and Mycology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akram Abouie Mehrizi
- , Malaria and Vector Research Group, Biotechnology Research Group, Pasteur Institute of Iran, Tehran, Iran.
| | - Asghar Fazaeli
- , Department of Parasitology and Mycology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Sedigheh Zakeri
- , Malaria and Vector Research Group, Biotechnology Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Navid Dinparast Djadid
- , Malaria and Vector Research Group, Biotechnology Research Group, Pasteur Institute of Iran, Tehran, Iran
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An engineered construct of cFLIP provides insight into DED1 structure and interactions. Structure 2022; 30:229-239.e5. [PMID: 34800372 PMCID: PMC8818036 DOI: 10.1016/j.str.2021.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 02/05/2023]
Abstract
Cellular FLICE-like inhibitory protein (cFLIP) is a member of the Death Domain superfamily with pivotal roles in many cellular processes and disease states, including cancer and autoimmune disorders. In the context of the death-inducing signaling complex (DISC), cFLIP isoforms regulate extrinsic apoptosis by controlling procaspase-8 activation. The function of cFLIP is mediated through a series of protein-protein interactions, engaging the two N-terminal death effector domains (DEDs). Here, we solve the structure of an engineered DED1 domain of cFLIP using solution nuclear magnetic resonance (NMR) and we define the interaction with FADD and calmodulin, protein-protein interactions that regulate the function of cFLIP in the DISC. cFLIP DED1 assumes a canonical DED fold characterized by six α helices and is able to bind calmodulin and FADD through two separate interfaces. Our results clearly demonstrate the role of DED1 in the cFLIP/FADD association and contribute to the understanding of the assembly of DISC filaments.
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Falak S, Sajed M, Rashid N. Strategies to enhance soluble production of heterologous proteins in Escherichia coli. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00994-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Emulsion Adjuvants for Use in Veterinary Vaccines. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2412:247-253. [PMID: 34918248 DOI: 10.1007/978-1-0716-1892-9_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The use of emulsion as adjuvants is widely used in veterinary vaccines. Emulsion adjuvants are inexpensive, stable, and relatively easy to prepare into vaccine formulations. Here we describe the preparation of oil-in-water emulsion adjuvant that has been shown to enhance immune responses and protect against diseases in pigs. This emulsion adjuvant and its variations could potentially be used alone or in combination with other adjuvants in veterinary vaccine formulations.
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Valdez N, Hughes C, Palmer SO, Sepulveda A, Dean FB, Escamilla Y, Bullard JM, Zhang Y. Rational Design of an Antimicrobial Peptide Based on Structural Insight into the Interaction of Pseudomonas aeruginosa Initiation Factor 1 with Its Cognate 30S Ribosomal Subunit. ACS Infect Dis 2021; 7:3161-3167. [PMID: 34709785 DOI: 10.1021/acsinfecdis.1c00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial infections continue to represent a major worldwide health hazard following the emergence of drug-resistant pathogenic strains. Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections with increased morbidity and mortality. The increasing antibiotic resistance in P. aeruginosa has led to an unmet need for discovery of new antibiotic candidates. Bacterial protein synthesis is an essential metabolic process and a validated target for antibiotic development; however, the precise structural mechanism in P. aeruginosa remains unknown. In this work, the interaction of P. aeruginosa initiation factor 1 (IF1) with the 30S ribosomal subunit was studied by NMR, which enabled us to construct a structure of IF1-bound 30S complex. A short α-helix in IF1 was found to be critical for IF1 ribosomal binding and function. A peptide derived from this α-helix was tested and displayed a high ability to inhibit bacterial growth. These results provide a clue for rational design of new antimicrobials.
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Affiliation(s)
- Nicolette Valdez
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Casey Hughes
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Stephanie O. Palmer
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Alyssa Sepulveda
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Frank B. Dean
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yaritza Escamilla
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - James M. Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
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Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation. Methods Enzymol 2021. [PMID: 34752287 DOI: 10.1016/bs.mie.2021.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D2O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D2O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.
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Chae YK, Kim H. Development of an Autoinducible Plasmid for Recombinant Protein Production. Protein Pept Lett 2021; 28:1398-1407. [PMID: 34749604 DOI: 10.2174/0929866528666211105113750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The production of recombinant proteins in E. coli involves such factors as host strains, expression vectors, culture media, and induction methods. The typical procedure to produce heterologous proteins consists of the following: (1) insertion of the target gene into a suitable vector to construct an overexpression plasmid, (2) transformation of a strain specialized for protein production with the constructed plasmid DNA, (3) growth of the host in a suitable medium and induction of the protein production at a right moment, and (4) further growth to get the maximum yield. There are hurdles involved in each of these steps, and researchers have developed many materials or methods, which often require special recipes or procedures. OBJECTIVE To eliminate the special requirements for the recombinant protein production by using readily available materials. Also to save time and effort in the routine protein production work. METHOD We started with a vector capable of producing a target protein fused to the C-terminus of the maltose binding protein (MBP). The mCherry (red fluorescent protein) gene was fused to MBP. It acted as a reporter in the initial screening procedure. The original lethal gene (barnase) was replaced with sacB. We chose 3 stationary phase promoters, and made hybrids of them by mixing halves from each one. The T5 promoter was replaced with these stationary phase promoters or their hybrids. The best plasmid was selected by the color intensity of the cell pellet. MBP and GST genes were inserted in place of sacB, and their production yields were compared with the original plasmid in the conventional way of expression. RESULTS We constructed an expression plasmid with an autoinducible promoter working in a host that was not specially designed for protein production and in a TB medium which did not contain any secret ingredient, nor was difficult to prepare unlike Studier's defined medium. This plasmid also contains a color indicator which turns red when protein production is successful. We tested our system with the maltose binding protein (MBP) and the glutathione S-transferase (GST), and showed that both proteins were produced to a level comparable to what the commercial medium and/or the specialized strain yielded. CONCLUSION We developed a plasmid equipped with an autoinducible promoter, a hybrid of the two promoters which were activated at the stationary phase. This plasmid does not need a special E. coli strain nor a sophisticated nor an expensive medium. It produces an intense red (or pink) color, which can be used as an indicator of a successful production of the target protein and as a predictive measure of the amount of the produced target protein. We speculate that this plasmid will have its greatest advantage when growing cells at low temperatures which would inevitably take a long time. .
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
| | - Hakbeom Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
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Abstract
A variety of effector proteins contribute to host defense in Caenorhabditis elegans. However, beyond lytic enzymes and antimicrobial peptides and proteins, little is known about the exact function of these infection-related effectors. This study set out to identify pathogen-dependent cytokine-like molecules, focusing on C-type lectin domain-containing proteins (CLECs). In total, 38 CLECs that are differentially regulated in response to bacterial infections have been previously identified by microarray and transcriptome sequencing (RNA-seq) analyses in C. elegans. We successfully cloned 18 of these 38 CLECs and chose to focus on CLEC-47 because, among these 18 cloned CLECs, it was the smallest protein and was recombinantly expressed at the highest levels in prokaryotic cells examined by SDS-PAGE. Quantitative real-time PCR (qRT-PCR/qPCR) showed that the expression of clec-47 was induced by a variety of Gram-positive bacterial pathogens, including Enterococcus faecium, Staphylococcus aureus, and Cutibacterium acnes, but was suppressed by the Gram-negative bacteria Klebsiella pneumoniae and Pseudomonas aeruginosa. By expressing CLEC-47 in HEK 293 cells, we showed that CLEC-47 is released into the culture media, which the Golgi apparatus inhibitors (brefeldin A [BFA] and GolgiStop) could block. Purified recombinant CLEC-47 (maltose binding protein [MBP]–CLEC-47–His) did not display antimicrobial activity against ESKAPE pathogen isolates but bound directly to murine macrophage J774A.1 cells. Recombinant CLEC-47 attracted and recruited J774A.1 cells in a chemotaxis assay. In addition, qPCR studies and enzyme-linked immunosorbent assays (ELISAs) showed that CLEC-47 activates J774A.1 cells in a dose- and time-dependent manner to express the proinflammatory cytokines tumor necrosis factor alpha (TNF-α), interleukin-1β (IL-1β), IL-6, and Macrophage Inflammatory Protein 2 (MIP-2). Moreover, C. elegans, fed with CLEC-47-expressing Escherichia coli, demonstrated enhanced expression of several antimicrobial proteins (CNC-1, CNC-2, CPR-1, and CPR-2) as well as the detoxification protein MTL-1. These data suggest that CLEC-47 functions as a novel cytokine-like signaling molecule and exemplify how the study of infection-related effectors in C. elegans can help elucidate the evolution of immune responses.
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Fan Q, Neubauer P, Gimpel M. Production of soluble regulatory hydrogenase from Ralstonia eutropha in Escherichia coli using a fed-batch-based autoinduction system. Microb Cell Fact 2021; 20:201. [PMID: 34663324 PMCID: PMC8522226 DOI: 10.1186/s12934-021-01690-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
Background Autoinduction systems can regulate protein production in Escherichia coli without the need to monitor cell growth or add inducer at the proper time following culture growth. Compared to classical IPTG induction, autoinduction provides a simple and fast way to obtain high protein yields. In the present study, we report on the optimization process for the enhanced heterologous production of the Ralstonia eutropha regulatory hydrogenase (RH) in E. coli using autoinduction. These autoinduction methods were combined with the EnPresso B fed-batch like growth system, which applies slow in situ enzymatic glucose release from a polymer to control cell growth and protein synthesis rate. Results We were able to produce 125 mg L−1 RH corresponding to a productivity averaged over the whole process time of 3 mg (L h)−1 in shake flasks using classic single-shot IPTG induction. IPTG autoinduction resulted in a comparable volumetric RH yield of 112 mg L−1 and due to the shorter overall process time in a 1.6-fold higher productivity of 5 mg (L h)−1. In contrast, lactose autoinduction increased the volumetric yield more than 2.5-fold and the space time yield fourfold reaching 280 mg L−1 and 11.5 mg (L h)−1, respectively. Furthermore, repeated addition of booster increased RH production to 370 mg L−1, which to our knowledge is the highest RH concentration produced in E. coli to date. Conclusions The findings of this study confirm the general feasibility of the developed fed-batch based autoinduction system and provide an alternative to conventional induction systems for efficient recombinant protein production. We believe that the fed-batch based autoinduction system developed herein will favor the heterologous production of larger quantities of difficult-to-express complex enzymes to enable economical production of these kinds of proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01690-4.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
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Aguilar Lucero D, Cantoia A, Ceccarelli EA, Rosano GL. Starting a new recombinant protein production project in Escherichia coli. Methods Enzymol 2021; 659:3-18. [PMID: 34752291 DOI: 10.1016/bs.mie.2021.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the goals in recombinant protein production in Escherichia coli is to maximize productivity. High volumetric and specific yields can be reached after careful selection of expression strains and optimization of cultivation parameters. In this chapter, we review the many tools available to make the most out of this versatile microbial cell factory. Useful guidelines and options for troubleshooting production are presented.
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Affiliation(s)
- Dianela Aguilar Lucero
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejo Cantoia
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Lokesha S, Ravi Kumar YS, Sujan Ganapathy PS, Gaur P, Arjun HM. Production of recombinant choline oxidase and its application in betaine production. 3 Biotech 2021; 11:410. [PMID: 34471592 DOI: 10.1007/s13205-021-02960-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/04/2021] [Indexed: 11/30/2022] Open
Abstract
Choline oxidase catalyzes the oxidation of choline to glycine betaine via betaine aldehyde in glycine betaine biosynthesis and betaine acts as an osmolyte. Choline oxidase has attracted a great deal of attention because of its wide application in clinical and its potential use in enzymatic betaine production. Therefore, the development of efficient methods for overexpression of choline oxidase will be very valuable. In the present study, the choline oxidase gene was amplified from a newly isolated Gram-positive soil Arthrobacter globiformis strain HYJE003 and was cloned into a pET expression vector. Furthermore, the culture conditions were optimized for overexpression of cloned choline oxidase gene in different hosts for periplasmic expression of the enzyme. Expression host system Rosetta-gami2(DE3)pLysS yielded more cell-free protein and 20 fold higher active enzyme compared to any other reported studies. Terrific Broth media were found to be yielding the highest cell biomass, by applying the optimized culture conditions and purification strategy 20,902 U of choline oxidase was produced with a specific activity of 95 U/mg. The optimum pH and temperature for the enzyme activity were found to be 7 and 37 °C, respectively. Finally, we have demonstrated efficient bioconversion of betaine using overexpressed and purified choline oxidase enzyme. The enzymatically produced betaine was estimated by the formation of betaine reineckate and we were able to produce 0.83 molar of betaine from one molar of choline chloride. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02960-z.
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Affiliation(s)
- S Lokesha
- Department of Biotechnology, M S Ramaiah Institute of Technology, MSR Nagar, Bangalore, Karnataka 560054 India
| | - Y S Ravi Kumar
- Department of Biotechnology, M S Ramaiah Institute of Technology, MSR Nagar, Bangalore, Karnataka 560054 India
| | - P S Sujan Ganapathy
- Nutrinorm Wellness Private Limited, No 508, 4th Floor, Medini, 60 Feet Road, Sahakarnagar, Bangalore, 560092 India
| | - Prashant Gaur
- Enzibeta Biotech Pvt. Ltd., IKP Knowledge Park, Genome Valley, Hyderabad, 500072 India
| | - H M Arjun
- Advanta Seeds Pvt. Ltd., Road No-7, Banjara Hills, Hyderabad, 500034 India
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Urniezius R, Kemesis B, Simutis R. Bridging Offline Functional Model Carrying Aging-Specific Growth Rate Information and Recombinant Protein Expression: Entropic Extension of Akaike Information Criterion. ENTROPY 2021; 23:e23081057. [PMID: 34441197 PMCID: PMC8393800 DOI: 10.3390/e23081057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/03/2022]
Abstract
This study presents a mathematical model of recombinant protein expression, including its development, selection, and fitting results based on seventy fed-batch cultivation experiments from two independent biopharmaceutical sites. To resolve the overfitting feature of the Akaike information criterion, we proposed an entropic extension, which behaves asymptotically like the classical criteria. Estimation of recombinant protein concentration was performed with pseudo-global optimization processes while processing offline recombinant protein concentration samples. We show that functional models including the average age of the cells and the specific growth at induction or the start of product biosynthesis are the best descriptors for datasets. We also proposed introducing a tuning coefficient that would force the modified Akaike information criterion to avoid overfitting when the designer requires fewer model parameters. We expect that a lower number of coefficients would allow the efficient maximization of target microbial products in the upstream section of contract development and manufacturing organization services in the future. Experimental model fitting was accomplished simultaneously for 46 experiments at the first site and 24 fed-batch experiments at the second site. Both locations contained 196 and 131 protein samples, thus giving a total of 327 target product concentration samples derived from the bioreactor medium.
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Walinda E, Morimoto D, Sorada T, Iwai K, Sugase K. Expression, solubility monitoring, and purification of the co-folded LUBAC LTM domain by structure-guided tandem folding in autoinducing cultures. Protein Expr Purif 2021; 187:105953. [PMID: 34390872 DOI: 10.1016/j.pep.2021.105953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
The linear ubiquitin chain assembly complex tethering motif (LUBAC-LTM) domain is composed of two different accessory LUBAC components (HOIL-1L and SHARPIN) but folds as a single globular domain. Targeted disruption of the intricate LTM-LTM interaction destabilizes LUBAC in lymphoma cells, thereby attenuating LUBAC stability, which highlights that targeting the interaction between the two LTM motifs is a promising strategy for the development of new agents against cancers that depend on LUBAC activity for their survival. To further screen for small-molecule inhibitors that can selectively disrupt the LTM-LTM interaction, it is necessary to obtain high-purity samples of the LTM domain. Ideally, such a sample would not contain any components other than the LTM itself, so that false positives (molecules binding to other parts of LUBAC) could be eliminated from the screening process. Here we report a simple strategy that enabled successful bacterial production of the isolated LUBAC LTM domain in high yield and at high purity. The strategy combines (1) structural analysis highlighting the possibility of tandem expression in the SHARPINL™ to HOIL-1LL™ direction; (2) bacterial expression downstream of EGFP to efficiently monitor expression and solubility; (3) gentle low-temperature folding using autoinduction. Formation of stably folded LTM was verified by size-exclusion chromatography and heteronuclear NMR spectroscopy. From 200-ml cultures sufficient quantities (∼7 mg) of high-purity protein for structural studies could be obtained. The presented strategy will be beneficial for LUBAC LTM-based drug-screening efforts and likely serve as a useful primer for similar cases, i.e., whenever a smaller folded fragment is to be isolated from a larger protein complex for site-specific downstream applications.
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Affiliation(s)
- Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tomoki Sorada
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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Schuster LA, Reisch CR. A plasmid toolbox for controlled gene expression across the Proteobacteria. Nucleic Acids Res 2021; 49:7189-7202. [PMID: 34125913 PMCID: PMC8266580 DOI: 10.1093/nar/gkab496] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Controlled gene expression is fundamental for the study of gene function and our ability to engineer bacteria. However, there is currently no easy-to-use genetics toolbox that enables controlled gene expression in a wide range of diverse species. To facilitate the development of genetics systems in a fast, easy, and standardized manner, we constructed and tested a plasmid assembly toolbox that will enable the identification of well-regulated promoters in many Proteobacteria and potentially beyond. Each plasmid is composed of four categories of genetic parts (i) the origin of replication, (ii) resistance marker, (iii) promoter-regulator and (iv) reporter. The plasmids can be efficiently assembled using ligation-independent cloning, and any gene of interest can be easily inserted in place of the reporter. We tested this toolbox in nine different Proteobacteria and identified regulated promoters with over fifty-fold induction range in eight of these bacteria. We also constructed variant libraries that enabled the identification of promoter-regulators with varied expression levels and increased inducible fold change relative to the original promoter. A selection of over 50 plasmids, which contain all of the toolbox's genetic parts, are available for community use and will enable easy construction and testing of genetics systems in both model and non-model bacteria.
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Affiliation(s)
- Layla A Schuster
- Dept. of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Christopher R Reisch
- Dept. of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA
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Recombinant production of Trx-Ib-AMP4 and Trx-E50-52 antimicrobial peptides and antimicrobial synergistic assessment on the treatment of methicillin-resistant Staphylococcus aureus under in vitro and in vivo situations. Protein Expr Purif 2021; 188:105949. [PMID: 34324967 DOI: 10.1016/j.pep.2021.105949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022]
Abstract
PURPOSE The production of alternative novel antimicrobial agents is considered an efficient way to cope with multidrug resistance among pathogenic bacteria. E50-52 and Ib-AMP4 antimicrobial peptides (AMPs) have illustrated great proven antibacterial effects. The aim of this study was recombinant production of these AMPs and investigation of their synergistic effects on methicillin-resistant Staphylococcus aureus (MRSA). METHOD At first, the codon optimized sequences of the Ib-AMP4 (UniProt: 024006 (PRO_0000020721), and E50-52 (UniProtKB: P85148) were individually ligated into the pET-32α vector and transformed into E. coli. After the optimization of production and purification steps, the MIC (Minimum inhibitory concentration), time kill and growth kinetic tests of recombinant proteins were determined against MRSA. Finally, the in vivo wound healing efficiency was tested. RESULTS AND CONCLUSION The recorded MIC of recombinant Trx-Ib-AMP4, Trx-E50-52 against MRSA bacterium were 0.375 and 0.0875 mg/mL respectively. The combination application of the produced AMPs by the checkerboard method confirmed their synergic activity. The results of the time-kill showed sharply decrease of the number of viable cells with over five time reductions in log10 CFU/mL by the combination of Trx-E50-52 and Trx-IbAMP4 at 2 × MIC within 240 min. The growth kinetic results confirmed the combination of Trx-E50-52 and Trx-IbAMP4 had much greater success in the reduction of over 50 % of MRSA suspensions' turbidity within the first hour. Wound healing assay and histological analysis of infected mice treated with Trx-Ib-AMP4 or Trx-E50-52 compared with those treated with a combination of Trx-Ib-AMP4 and Trx-E50-52 showed significant synergic effects.
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Frankel R, Bernfur K, Sparr E, Linse S. Purification and HDL-like particle formation of apolipoprotein A-I after co-expression with the EDDIE mutant of Npro autoprotease. Protein Expr Purif 2021; 187:105946. [PMID: 34298139 DOI: 10.1016/j.pep.2021.105946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/23/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023]
Abstract
Apolipoprotein A-I (ApoA-I) is the major protein constituent of high-density lipoprotein particles, and as such is involved in cholesterol transport and activation of LCAT (the lecithin:cholesterol acyltransferase). It may also form amyloidal deposits in the body, showing the multifaceted interactions of ApoA-I. In order to facilitate the study of ApoA-I in various systems, we have developed a protocol based on recombinant expression in E. coli. ApoA-I is protected from degradation by driving its expression to inclusion bodies using a tag: the EDDIE mutant of Npro autoprotease from classical swine fever virus. Upon refolding, EDDIE will cleave itself off from the target protein. The result is a tag-free ApoA-I, with its N-terminus intact. ApoA-I was then purified using a five-step procedure composed of anion exchange chromatography, immobilized metal ion affinity chromatography, hydrophobic interaction chromatography, boiling and size exclusion chromatography. This led to protein of high purity as confirmed with SDS-PAGE and mass spectrometry. The purified ApoA-I formed discoidal objects in the presence of zwitterionic phospholipid DMPC, showing its retained function of interacting with lipids. The protocol was also tested by expression and purification of two ApoA-I mutants, both of which could be purified in the same manner as the wildtype, showing the robustness of the protocol.
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Affiliation(s)
- Rebecca Frankel
- Department of Biochemistry and Structural Biology, Lund University, P O Box 124, SE22100, Lund, Sweden; Department of Physical Chemistry, Lund University, P O Box 124, SE22100, Lund, Sweden.
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Lund University, P O Box 124, SE22100, Lund, Sweden
| | - Emma Sparr
- Department of Physical Chemistry, Lund University, P O Box 124, SE22100, Lund, Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, P O Box 124, SE22100, Lund, Sweden.
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Sanchez-Alvarez K, Rosales-Mendoza S, Reyes-Barrera KL, Moreno-Fierros L, Soria-Guerra RE, Castillo-Collazo R, Monreal-Escalente E, Alpuche-Solis AG. Antibodies induced by oral immunization of mice with a recombinant protein produced in tobacco plants harboring Bordetella pertussis epitopes. PLANT CELL, TISSUE AND ORGAN CULTURE 2021; 147:85-96. [PMID: 34276113 PMCID: PMC8272453 DOI: 10.1007/s11240-021-02107-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Bordetella pertusis causes whooping cough or pertussis, disease that has not been eradicated and is reemerging despite the availability and massive application for decades of vaccines, such as Boostrix® which is an acellular vaccine harboring two regions of S1 subunit of the pertussis toxin, one region of filamentous hemagglutinin and one region of pertactin. In 2008, the World Health Organization estimated 16 million new cases and 95% occurred in developing countries with 195,000 children's deaths. We attempt to improve the vaccine against whooping cough and reduce its production costs by obtaining plants and bacteria expressing a heterologous protein harboring pertactin, pertussis toxin, and filamentous hemagglutinin epitopes from B. pertussis and assessing its immunogenicity after oral administration to mice. First, we designed a synthetic gene that encodes a multiepitope, then it was cloned into a vector for transient transformation by infiltration of tobacco plants with low amounts of nicotine; the codon bias-optimized construct was also cloned into an Escherichia coli expression vector. Recombinant proteins from E. coli cells (PTF) and tobacco leaves (PTF-M3') were purified by nickel affinity with a yield of 0.740 mg of recombinant protein per g dry weight. Purified recombinant proteins were administered orally to groups of Balb/c mice using the Boostrix® vaccine and vehicle (PBS) as positive and negative controls, respectively. A higher mucosal and systemic antibody responses were obtained in mice receiving the PTF and PTF-M3' proteins than Boostrix® or PBS. These findings prove the concept that oral administration of multiepitope recombinant proteins expressed in plants may be a potential edible vaccine. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11240-021-02107-1.
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Affiliation(s)
- Karla Sanchez-Alvarez
- División de Biología Molecular, IPICYT, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P. México
| | - Sergio Rosales-Mendoza
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, 78210 San Luis Potosí, S.L.P. México
| | - Karen L. Reyes-Barrera
- División de Biología Molecular, IPICYT, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P. México
| | - Leticia Moreno-Fierros
- Inmunidad en Mucosas, UBIMED, FES-Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios 1, 54090 Tlalnepantla, México
| | - Ruth E. Soria-Guerra
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, 78210 San Luis Potosí, S.L.P. México
| | - Rosalba Castillo-Collazo
- División de Biología Molecular, IPICYT, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P. México
| | - Elizabeth Monreal-Escalente
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, 78210 San Luis Potosí, S.L.P. México
| | - Angel G. Alpuche-Solis
- División de Biología Molecular, IPICYT, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P. México
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