1887

Riboflavin Riboswitch Regulation: Hands-On Learning about the Role of RNA Structures in the Control of Gene Expression in Bacteria

    Authors: Catherine E. Vrentas1,*, Jacob J. Adler2, Adam J. Kleinschmit3, Julia Massimelli4
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: The Engaged Scientist, Ames, IA, 50014; 2: Division of Mathematics and Natural Sciences, Brescia University, Owensboro, KY, 42301; 3: Department of Biology and Earth Sciences, Adams State University, Alamosa, CO, 81101; 4: Department of Molecular Biology and Biochemistry, University of California – Irvine, Irvine, CA, 92697
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 09 October 2017 Accepted 29 January 2018 Published 25 May 2018
    • ©2018 Author(s). Published by the American Society for Microbiology.
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: The Engaged Scientist, 332 Sunflower Drive, Ames, IA, 50014. Phone: 814-883-8581. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. May 2018 vol. 19 no. 2 doi:10.1128/jmbe.v19i2.1501
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    Abstract:

    American Society for Microbiology (ASM) Curriculum Guidelines highlight the importance of instruction about informational flow in organisms, including regulation of gene expression. However, foundational central dogma concepts and more advanced gene regulatory mechanisms are challenging for undergraduate biology students. To increase student comprehension of these principles, we designed an activity for upper-level biology students centered on construction and analysis of physical models of bacterial riboswitches. Students manipulate an inexpensive bag of supplies (beads, pipe cleaners) to model two conformations of a riboswitch in a bacterial transcript. After initial pilot testing, we implemented the activity in three upper-level classes at one research-intensive and two primarily undergraduate institutions. To assess student perceptions of learning gains, we utilized a pre/post-activity 5-point Likert-type survey instrument to characterize student perceptions of confidence in both their understanding of riboswitches and their ability to apply the central dogma to riboswitches. Median post-test ranks were significantly higher than median pre-test ranks ( < 0.0001) when compared by the Wilcoxon signed-rank test ( = 31). Next, we assessed post-activity knowledge via use of a rubric to score student responses on exam questions. More than 80% of students could correctly describe and diagram examples of riboswitches; data from initial iterations were used to enhance curriculum materials for subsequent implementations. We conclude that this riboswitch activity leads to both student-reported increases in confidence in the ASM curriculum dimension of gene regulation, including central dogma concepts, and demonstrated student ability to diagram riboswitches, predict outcomes of riboswitches, and connect riboswitches to evolutionary roles.

References & Citations

1. Merkel S ASM Task Force on Curriculum Guidelines for Undergraduate Microbiology 2012 The development of curricular guidelines for introductory microbiology that focus on understanding J Microbiol Biol Educ 13 32 10.1128/jmbe.v13i1.363 http://dx.doi.org/10.1128/jmbe.v13i1.363
2. Serganov A, Patel DJ 2012 Metabolite recognition principles and molecular mechanisms underlying riboswitch function Annu Rev Biophys 41 343 370 10.1146/annurev-biophys-101211-113224 http://dx.doi.org/10.1146/annurev-biophys-101211-113224
3. Nudler E, Mironov AS 2004 The riboswitch control of bacterial metabolism Trends Biochem Sci 29 11 17 10.1016/j.tibs.2003.11.004 http://dx.doi.org/10.1016/j.tibs.2003.11.004
4. Winkler WC, Breaker RR 2005 Regulation of bacterial gene expression by riboswitches Annu Rev Microbiol 59 487 517 10.1146/annurev.micro.59.030804.121336 http://dx.doi.org/10.1146/annurev.micro.59.030804.121336
5. Breaker RR 2009 Riboswitches: from ancient gene-control systems to modern drug targets Future Microbiol 4 771 773 10.2217/fmb.09.46 http://dx.doi.org/10.2217/fmb.09.46
6. Serganov A, Nudler E 2013 A decade of riboswitches Cell 152 17 24 10.1016/j.cell.2012.12.024 http://dx.doi.org/10.1016/j.cell.2012.12.024
7. Sherwood AV, Henkin TM 2016 Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses Annu Rev Microbiol 70 361 374 10.1146/annurev-micro-091014-104306 http://dx.doi.org/10.1146/annurev-micro-091014-104306
8. Tucker BJ, Breaker RR 2005 Riboswitches as versatile gene control elements Curr Opin Struct Biol 15 342 348 10.1016/j.sbi.2005.05.003 http://dx.doi.org/10.1016/j.sbi.2005.05.003
9. Freeman S, Eddy S, McDonough M, Smith M, Okoroafor N, Jordt H, Wenderoth M 2014 Active learning increases student performance in science, engineering, and mathematics Proc Natl Acad Sci 111 8410 8415 10.1073/pnas.1319030111 http://dx.doi.org/10.1073/pnas.1319030111
10. Van Driel FH, Verloop N 2002 Experienced teachers’ knowledge of teaching and learning of models and modelling in science education Int J Sci Educ 24 1255 1272 10.1080/09500690210126711 http://dx.doi.org/10.1080/09500690210126711
11. Perkins KK, Loeblein PJ, Dessau KL 2010 SIMS for science Sci Teach 77 46
12. Stefanski KM, Gardner GE, Seipelt-Thiemann RL 2016 Development of a lac operon concept inventory (LOCI) CBE Life Sci Educ 15 ar24 10.1187/cbe.15-07-0162 http://dx.doi.org/10.1187/cbe.15-07-0162
13. Cooper RA 2015 Teaching the big ideas of biology with operon models Am Biol Teach 77 30 33 10.1525/abt.2015.77.1.5 http://dx.doi.org/10.1525/abt.2015.77.1.5
14. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS 2002 Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation Nucleic Acids Res 30 3141 3151 10.1093/nar/gkf433 http://dx.doi.org/10.1093/nar/gkf433
15. Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA 1999 A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes Trends Genet 15 439 442 10.1016/S0168-9525(99)01856-9 http://dx.doi.org/10.1016/S0168-9525(99)01856-9
16. Priano C 2013 Shaping tRNA Am Biol Teach 75 708 709 10.1525/abt.2013.75.9.14 http://dx.doi.org/10.1525/abt.2013.75.9.14
17. Oliva G, Sahr T, Buchrieser C 2015 Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence FEMS Microbiol Rev 39 331 349 10.1093/femsre/fuv022 http://dx.doi.org/10.1093/femsre/fuv022
18. Lee ER, Blount KF, Breaker RR 2009 Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression RNA Biol 6 187 194 10.4161/rna.6.2.7727 http://dx.doi.org/10.4161/rna.6.2.7727
19. Serganov A, Huang L, Patel DJ 2009 Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Nature 458 233 237 10.1038/nature07642 http://dx.doi.org/10.1038/nature07642
20. Ott E, Stolz J, Lehmann M, Mack M 2009 The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis RNA Biol 6 276 280 10.4161/rna.6.3.8342 http://dx.doi.org/10.4161/rna.6.3.8342
21. Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, Malinverni JC, Mayhood T, Villafania A, Nahvi A, Murgolo N, Barbieri CM, Mann PA, Carr D, Xia E, Zuck P, Riley D, Painter RE, Walker SS, Sherborne B, de Jesus R, Pan W, Plotkin MA, Wu J, Rindgen D, Cummings J, Garlisi CG, Zhang R, Sheth PR, Gill CJ, Tang H, Roemer T 2015 Selective small-molecule inhibition of an RNA structural element Nature 526 672 677 10.1038/nature15542 http://dx.doi.org/10.1038/nature15542
22. Winkler WC, Cohen-Chalamish S, Breaker RR 2002 An mRNA structure that controls gene expression by binding FMN Proc Natl Acad Sci 99 15908 15913 10.1073/pnas.212628899 http://dx.doi.org/10.1073/pnas.212628899
23. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E 2002 Sensing small molecules by nascent DNA: a mechanism to control transcription in bacteria Cell 111 747 756 10.1016/S0092-8674(02)01134-0 http://dx.doi.org/10.1016/S0092-8674(02)01134-0
24. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE 2000 The protein data bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 http://dx.doi.org/10.1093/nar/28.1.235

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2018-05-25
2019-10-21

Abstract:

American Society for Microbiology (ASM) Curriculum Guidelines highlight the importance of instruction about informational flow in organisms, including regulation of gene expression. However, foundational central dogma concepts and more advanced gene regulatory mechanisms are challenging for undergraduate biology students. To increase student comprehension of these principles, we designed an activity for upper-level biology students centered on construction and analysis of physical models of bacterial riboswitches. Students manipulate an inexpensive bag of supplies (beads, pipe cleaners) to model two conformations of a riboswitch in a bacterial transcript. After initial pilot testing, we implemented the activity in three upper-level classes at one research-intensive and two primarily undergraduate institutions. To assess student perceptions of learning gains, we utilized a pre/post-activity 5-point Likert-type survey instrument to characterize student perceptions of confidence in both their understanding of riboswitches and their ability to apply the central dogma to riboswitches. Median post-test ranks were significantly higher than median pre-test ranks ( < 0.0001) when compared by the Wilcoxon signed-rank test ( = 31). Next, we assessed post-activity knowledge via use of a rubric to score student responses on exam questions. More than 80% of students could correctly describe and diagram examples of riboswitches; data from initial iterations were used to enhance curriculum materials for subsequent implementations. We conclude that this riboswitch activity leads to both student-reported increases in confidence in the ASM curriculum dimension of gene regulation, including central dogma concepts, and demonstrated student ability to diagram riboswitches, predict outcomes of riboswitches, and connect riboswitches to evolutionary roles.

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Figures

Image of FIGURE 1

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FIGURE 1

Riboswitch structures. Photographed models with the riboswitch in the ON (A) and OFF (B) conformations, respectively. Student groups were asked to assemble two models of the riboswitch using lettered pony beads (A, G, C, and U) to show base pairing of mRNA. The sequence and base pairing instructions were provided in a PowerPoint presentation ( Appendix 4 ) or as a handout ( Appendix 6 ). (A) A base pairing conformation that does not involve the start codon (AUG, right end of green pipe cleaner). The blue bead depicted in (B) represents the ligand binding. The ligand promotes a conformation change in the base pairing in the RNA. In the OFF conformation, the AUG codon is inaccessible due to interactions with other bases as part of a hairpin structure (second hairpin on the red pipe cleaner).

Source: J. Microbiol. Biol. Educ. May 2018 vol. 19 no. 2 doi:10.1128/jmbe.v19i2.1501
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