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Bechard ME, Farahani P, Greene D, Pham A, Orry A, Rasche ME. Purification, kinetic characterization, and site-directed mutagenesis of Methanothermobacter thermautotrophicus RFAP Synthase Produced in Escherichia coli. AIMS Microbiol 2019; 5:186-204. [PMID: 31663056 PMCID: PMC6787355 DOI: 10.3934/microbiol.2019.3.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
Methane-producing archaea are among a select group of microorganisms that utilize tetrahydromethanopterin (H4MPT) as a one-carbon carrier instead of tetrahydrofolate. In H4MPT biosynthesis, β-ribofuranosylaminobenzene 5'-phosphate (RFAP) synthase catalyzes the production of RFAP, CO2, and pyrophosphate from p-aminobenzoic acid (pABA) and phosphoribosyl-pyrophosphate (PRPP). In this work, to gain insight into amino acid residues required for substrate binding, RFAP synthase from Methanothermobacter thermautotrophicus was produced in Escherichia coli, and site-directed mutagenesis was used to alter arginine 26 (R26) and aspartic acid 19 (D19), located in a conserved sequence of amino acids resembling the pABA binding site of dihydropteroate synthase. Replacement of R26 with lysine increased the KM for pABA by an order of magnitude relative to wild-type enzyme without substantially altering the KM for PRPP. Although replacement of D19 with alanine produced inactive enzyme, asparagine substitution allowed retention of some activity, and the K M for pABA increased about threefold relative to wild-type enzyme. A molecular model developed by threading RFAP synthase onto the crystal structure of homoserine kinase places R26 in the proposed active site. In the static model, D19 is located close to the active site, yet appears too far away to influence ligand binding directly. This may be indicative of the protein conformational change predicted previously in the Bi-Ter kinetic mechanism and/or formation of the active site at the interface of two subunits. Due to the vital role of RFAP synthase in H4MPT biosynthesis, insights into the mode of substrate binding and mechanism could be beneficial for developing RFAP synthase inhibitors designed to reduce the production of methane as a greenhouse gas.
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Affiliation(s)
- Matthew E Bechard
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Payam Farahani
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
| | - Dina Greene
- Northern California Regional Laboratories, The Permanente Medical Group, Berkeley, CA 94710
| | - Anna Pham
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
| | - Andrew Orry
- Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, CA 92121
| | - Madeline E Rasche
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
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Provost JJ, Bell JK, Bell JE. Development and Use of CUREs in Biochemistry. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1337.ch007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joseph J. Provost
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
| | - Jessica K. Bell
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
| | - John E. Bell
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
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Wang JTH. Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support. FEMS Microbiol Lett 2018; 364:4033031. [PMID: 28859321 DOI: 10.1093/femsle/fnx157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/21/2017] [Indexed: 12/20/2022] Open
Abstract
Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research.
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Affiliation(s)
- Jack T H Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Lefurgy ST, Mundorff EC. A 13-week research-based biochemistry laboratory curriculum. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 45:437-448. [PMID: 28251763 DOI: 10.1002/bmb.21054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/15/2017] [Accepted: 02/12/2017] [Indexed: 06/06/2023]
Abstract
Here, we present a 13-week research-based biochemistry laboratory curriculum designed to provide the students with the experience of engaging in original research while introducing foundational biochemistry laboratory techniques. The laboratory experience has been developed around the directed evolution of an enzyme chosen by the instructor, with mutations designed by the students. Ideal enzymes for this curriculum are able to be structurally modeled, solubly expressed, and monitored for activity by UV/Vis spectroscopy, and an example curriculum for haloalkane dehalogenase is given. Unique to this curriculum is a successful implementation of saturation mutagenesis and high-throughput screening of enzyme function, along with bioinformatics analysis, homology modeling, structural analysis, protein expression and purification, polyacrylamide gel electrophoresis, UV/Vis spectroscopy, and enzyme kinetics. Each of these techniques is carried out using a novel student-designed mutant library or enzyme variant unique to the lab team and, importantly, not described previously in the literature. Use of a well-established set of protocols promotes student data quality. Publication may result from the original student-generated hypotheses and data, either from the class as a whole or individual students that continue their independent projects upon course completion. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):437-448, 2017.
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Affiliation(s)
- Scott T Lefurgy
- Department of Chemistry, Hofstra University, 151 Hofstra University, Hempstead, NY, 11549
| | - Emily C Mundorff
- Department of Chemistry, Hofstra University, 151 Hofstra University, Hempstead, NY, 11549
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Brown AM, Lewis SN, Bevan DR. Development of a structured undergraduate research experience: Framework and implications. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:463-474. [PMID: 27124101 DOI: 10.1002/bmb.20975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/30/2016] [Accepted: 03/03/2016] [Indexed: 06/05/2023]
Abstract
Participating in undergraduate research can be a pivotal experience for students in life science disciplines. Development of critical thinking skills, in addition to conveying scientific ideas in oral and written formats, is essential to ensuring that students develop a greater understanding of basic scientific knowledge and the research process. Modernizing the current life sciences research environment to accommodate the growing demand by students for experiential learning is needed. By developing and implementing a structured, theory-based approach to undergraduate research in the life sciences, specifically biochemistry, it has been successfully shown that more students can be provided with a high-quality, high-impact research experience. The structure of this approach allowed students to develop novel, independent projects in a computational molecular modeling lab. Students engaged in an experience in which career goals, problem-solving skills, time management skills, and independence in a research lab were developed. After experiencing this approach to undergraduate research, students reported feeling challenged to think critically and prepared for future career paths. The approach allowed for a progressive learning environment where more undergraduate students could participate in publishable research. Future areas for development include implementation in a bench-top lab and extension to disciplines beyond biochemistry. In this study, it has been shown that utilizing the structured approach to undergraduate research could allow for more students to experience undergraduate research and develop into more confident, independent life scientists well prepared for graduate schools and professional research environments. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):463-474, 2016.
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Affiliation(s)
- Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, 24061, Virginia
| | - Stephanie N Lewis
- Office of Undergraduate Academic Affairs, Virginia Tech, Blacksburg, 24061, Virginia
| | - David R Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, 24061, Virginia.
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Freitas MJ, Silva JV, Korrodi-Gregório L, Fardilha M. Non-stop lab week: A real laboratory experience for life sciences postgraduate courses. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:297-303. [PMID: 26891775 DOI: 10.1002/bmb.20947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 10/27/2015] [Accepted: 11/29/2015] [Indexed: 06/05/2023]
Abstract
At the Portuguese universities, practical classes of life sciences are usually professor-centered 2-hour classes. This approach results in students underprepared for a real work environment in a research/clinical laboratory. To provide students with a real-life laboratory environment, the Non-Stop Lab Week (NSLW) was created in the Molecular Biomedicine master program at the University of Aveiro, Portugal. The unique feature of the NSLW is its intensity: during a 1-week period, students perform a subcloning and a protein expression project in an environment that mimics a real laboratory. Students work autonomously, and the progression of work depends on achieving the daily goals. Throughout the three curricular years, most students considered the intensity of the NSLW a very good experience and fundamental for their future. Moreover, after some experience in a real laboratory, students state that both the techniques and the environment created in the NSLW were similar to what they experience in their current work situation. The NSLW fulfills a gap in postgraduate students' learning, particularly in practical skills and scientific thinking. Furthermore, the NSLW experience provides skills to the students that are crucial to their future research area. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:297-303, 2016.
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Affiliation(s)
- Maria João Freitas
- Signal Transduction Laboratory, iBiMED-Institute for Research in Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Joana Vieira Silva
- Signal Transduction Laboratory, iBiMED-Institute for Research in Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Luís Korrodi-Gregório
- Signal Transduction Laboratory, iBiMED-Institute for Research in Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
- Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, 08907, Spain
| | - Margarida Fardilha
- Signal Transduction Laboratory, iBiMED-Institute for Research in Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
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Adams DJ. Current Trends in Laboratory Class Teaching in University Bioscience Programmes. ACTA ACUST UNITED AC 2015. [DOI: 10.3108/beej.13.3] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David J. Adams
- UK Centre for Bioscience, Higher Education Academy, and Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT
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Muth GW, Chihade JW. A streamlined molecular biology module for undergraduate biochemistry labs. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 36:209-216. [PMID: 21591193 DOI: 10.1002/bmb.20170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Site-directed mutagenesis and other molecular biology techniques, including plasmid manipulation and restriction analysis, are commonly used tools in the biochemistry research laboratory. In redesigning our biochemistry lab curricula, we sought to integrate these techniques into a term-long, project-based course. In the module presented here, students use structural data to design a site-directed mutant and make the mutation using the Künkel method. A second, silent mutant, that creates or removes a restriction site, is simultaneously introduced. Restriction digestion and agarose gel electrophoresis are used to assess the success of mutagenesis. Placing these procedures in the context of continuous, student-driven project serves to create a “research style” laboratory environment.
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Affiliation(s)
- Gregory W Muth
- Department of Chemistry, St. Olaf College, Northfield, Minnesota, USA.
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Henderson L, Buising C, Wall P. Teaching undergraduate research: The one-room schoolhouse model. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 36:28-33. [PMID: 21591156 DOI: 10.1002/bmb.20134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Undergraduate research in the biochemistry, cell, and molecular biology program at Drake University uses apprenticeship, cooperative-style learning, and peer mentoring in a cross-disciplinary and cross-community educational program. We call it the one-room schoolhouse approach to teaching undergraduate research. This approach is cost effective, aids learning, supports the development of science and transferable management skills, is productive, and supports diversity. It allows a small set of faculty to involve large numbers of students in research and maintain a productive scholarship program. It provides students with skills in scientific research and transferable skills that they apply to a wide set of careers.
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Affiliation(s)
- Larhee Henderson
- Biochemistry, Cell and Molecular Biology Program, Drake University, Des Moines, Iowa.
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