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
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • HTML
    55.18 Kb
  • PDF
    396.51 Kb
  • XML
    63.57 Kb

    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 SASM Task Force on Curriculum Guidelines for Undergraduate Microbiology2012The development of curricular guidelines for introductory microbiology that focus on understandingJ Microbiol Biol Educ133210.1128/jmbe.v13i1.363 http://dx.doi.org/10.1128/jmbe.v13i1.363
2. Serganov A, Patel DJ2012Metabolite recognition principles and molecular mechanisms underlying riboswitch functionAnnu Rev Biophys4134337010.1146/annurev-biophys-101211-113224 http://dx.doi.org/10.1146/annurev-biophys-101211-113224
3. Nudler E, Mironov AS2004The riboswitch control of bacterial metabolismTrends Biochem Sci29111710.1016/j.tibs.2003.11.004 http://dx.doi.org/10.1016/j.tibs.2003.11.004
4. Winkler WC, Breaker RR2005Regulation of bacterial gene expression by riboswitchesAnnu Rev Microbiol5948751710.1146/annurev.micro.59.030804.121336 http://dx.doi.org/10.1146/annurev.micro.59.030804.121336
5. Breaker RR2009Riboswitches: from ancient gene-control systems to modern drug targetsFuture Microbiol477177310.2217/fmb.09.46 http://dx.doi.org/10.2217/fmb.09.46
6. Serganov A, Nudler E2013A decade of riboswitchesCell152172410.1016/j.cell.2012.12.024 http://dx.doi.org/10.1016/j.cell.2012.12.024
7. Sherwood AV, Henkin TM2016Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responsesAnnu Rev Microbiol7036137410.1146/annurev-micro-091014-104306 http://dx.doi.org/10.1146/annurev-micro-091014-104306
8. Tucker BJ, Breaker RR2005Riboswitches as versatile gene control elementsCurr Opin Struct Biol1534234810.1016/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 M2014Active learning increases student performance in science, engineering, and mathematicsProc Natl Acad Sci1118410841510.1073/pnas.1319030111 http://dx.doi.org/10.1073/pnas.1319030111
10. Van Driel FH, Verloop N2002Experienced teachers’ knowledge of teaching and learning of models and modelling in science educationInt J Sci Educ241255127210.1080/09500690210126711 http://dx.doi.org/10.1080/09500690210126711
11. Perkins KK, Loeblein PJ, Dessau KL2010SIMS for scienceSci Teach7746
12. Stefanski KM, Gardner GE, Seipelt-Thiemann RL2016Development of a lac operon concept inventory (LOCI)CBE Life Sci Educ15ar2410.1187/cbe.15-07-0162 http://dx.doi.org/10.1187/cbe.15-07-0162
13. Cooper RA2015Teaching the big ideas of biology with operon modelsAm Biol Teach77303310.1525/abt.2015.77.1.5 http://dx.doi.org/10.1525/abt.2015.77.1.5
14. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS2002Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuationNucleic Acids Res303141315110.1093/nar/gkf433 http://dx.doi.org/10.1093/nar/gkf433
15. Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA1999A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genesTrends Genet1543944210.1016/S0168-9525(99)01856-9 http://dx.doi.org/10.1016/S0168-9525(99)01856-9
16. Priano C2013Shaping tRNAAm Biol Teach7570870910.1525/abt.2013.75.9.14 http://dx.doi.org/10.1525/abt.2013.75.9.14
17. Oliva G, Sahr T, Buchrieser C2015Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulenceFEMS Microbiol Rev3933134910.1093/femsre/fuv022 http://dx.doi.org/10.1093/femsre/fuv022
18. Lee ER, Blount KF, Breaker RR2009Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expressionRNA Biol618719410.4161/rna.6.2.7727 http://dx.doi.org/10.4161/rna.6.2.7727
19. Serganov A, Huang L, Patel DJ2009Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitchNature45823323710.1038/nature07642 http://dx.doi.org/10.1038/nature07642
20. Ott E, Stolz J, Lehmann M, Mack M2009The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensisRNA Biol627628010.4161/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 T2015Selective small-molecule inhibition of an RNA structural elementNature52667267710.1038/nature15542 http://dx.doi.org/10.1038/nature15542
22. Winkler WC, Cohen-Chalamish S, Breaker RR2002An mRNA structure that controls gene expression by binding FMNProc Natl Acad Sci99159081591310.1073/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 E2002Sensing small molecules by nascent DNA: a mechanism to control transcription in bacteriaCell11174775610.1016/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 PE2000The protein data bankNucleic Acids Res2823524210.1093/nar/28.1.235 http://dx.doi.org/10.1093/nar/28.1.235

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v19i2.1501
2018-05-25
2018-08-17

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.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/jmbe/19/2/jmbe-19-64.html?itemId=/content/journal/jmbe/10.1128/jmbe.v19i2.1501&mimeType=html&fmt=ahah

Figures

Image of FIGURE 1

Click to view

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
Download as Powerpoint

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error