ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria

View Author Information
† ‡ § Department of Molecular Biophysics and Biochemistry, Department of Molecular, Cellular, and Developmental Biology, and §Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, United States
Cite this: Biochemistry 2017, 56, 2, 359–363
Publication Date (Web):December 21, 2016
Copyright © 2016 American Chemical Society

    Article Views





    Other access options
    Supporting Info (1)»


    Abstract Image

    Recently, it was determined that representatives of the riboswitch candidates called ykkC and mini-ykkC directly bind free guanidine. These riboswitches regulate the expression of genes whose protein products are implicated in overcoming the toxic effects of this ligand. Thus, the relevant ykkC motif and mini-ykkC motif RNAs have been classified as guanidine-I and guanidine-II riboswitch RNAs, respectively. Moreover, we had previously noted that a third candidate riboswitch class, called ykkC-III, was associated with a distribution of genes similar to those of the other two motifs. Therefore, it was predicted that ykkC-III motif RNAs would sense and respond to the same ligand. In this report, we present biochemical data supporting the hypothesis that ykkC-III RNAs represent a third class of guanidine-sensing RNAs called guanidine-III riboswitches. Members of the guanidine-III riboswitch class bind their ligand with an affinity similar to that observed for members of the other two classes. Notably, there are some sequence similarities between guanidine-II and guanidine-III riboswitches. However, the characteristics of ligand discrimination by guanidine-III RNAs are different from those of the other guanidine-binding motifs, suggesting that the binding pockets have distinct features among the three riboswitch classes.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.


    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.biochem.6b01271.

    • Figures S1–S6 and Table S1 (PDF)

    Terms & Conditions

    Electronic Supporting Information files are available without a subscription to ACS Web Editions. The American Chemical Society holds a copyright ownership interest in any copyrightable Supporting Information. Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website, either in whole or in part, in either machine-readable form or any other form without permission from the American Chemical Society. For permission to reproduce, republish and redistribute this material, requesters must process their own requests via the RightsLink permission system. Information about how to use the RightsLink permission system can be found at

    Cited By

    This article is cited by 68 publications.

    1. Kushal Singh, Govardhan Reddy. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. Journal of Chemical Theory and Computation 2024, 20 (1) , 421-435.
    2. Ronald R. Breaker. The Biochemical Landscape of Riboswitch Ligands. Biochemistry 2022, 61 (3) , 137-149.
    3. Indu Negi, Amanpreet Singh Mahmi, Preethi Seelam Prabhakar, Purshotam Sharma. Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands. Journal of Chemical Information and Modeling 2021, 61 (10) , 5243-5255.
    4. Peter J. F. Henderson, Claire Maher, Liam D. H. Elbourne, Bart A. Eijkelkamp, Ian T. Paulsen, Karl A. Hassan. Physiological Functions of Bacterial “Multidrug” Efflux Pumps. Chemical Reviews 2021, 121 (9) , 5417-5478.
    5. Sudeshna Manna, Johnny Truong, Ming C. Hammond. Guanidine Biosensors Enable Comparison of Cellular Turn-on Kinetics of Riboswitch-Based Biosensor and Reporter. ACS Synthetic Biology 2021, 10 (3) , 566-578.
    6. Hubert Salvail, Aparaajita Balaji, Diane Yu, Adam Roth, Ronald R. Breaker. Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria. Biochemistry 2020, 59 (49) , 4654-4662.
    7. Nicholas O. Schneider, Lambros J. Tassoulas, Danyun Zeng, Amanda J. Laseke, Nicholas J. Reiter, Lawrence P. Wackett, Martin St. Maurice. Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine. Biochemistry 2020, 59 (35) , 3258-3270.
    8. Ronald R. Breaker. Imaginary Ribozymes. ACS Chemical Biology 2020, 15 (8) , 2020-2030.
    9. Madeline E. Sherlock, Harini Sadeeshkumar, Ronald R. Breaker. Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates. Biochemistry 2019, 58 (5) , 401-410.
    10. Ronald R. Breaker, Ruben M. Atilho, Sarah N. Malkowski, James W. Nelson, and Madeline E. Sherlock . The Biology of Free Guanidine As Revealed by Riboswitches. Biochemistry 2017, 56 (2) , 345-347.
    11. Madeline E. Sherlock, Sarah N. Malkowski, and Ronald R. Breaker . Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria. Biochemistry 2017, 56 (2) , 352-358.
    12. Ekaterina Frantsuzova, Alexander Bogun, Olga Kopylova, Anna Vetrova, Inna Solyanikova, Rostislav Streletskii, Yanina Delegan. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. Biology 2024, 13 (5) , 339.
    13. Dietmar Funck, Malte Sinn, Giuseppe Forlani, Jörg S Hartig. Guanidine production by plant homoarginine-6-hydroxylases. eLife 2024, 12
    14. Dietmar Funck, Malte Sinn, Giuseppe Forlani, Jörg S Hartig. Guanidine production by plant homoarginine-6-hydroxylases. eLife 2024, 12
    15. Dietmar Funck, Malte Sinn, Giuseppe Forlani, Jörg S. Hartig. Guanidine Production by Plant Homoarginine-6-hydroxylases. 2024
    16. Felina Lenkeit, Iris Eckert, Malte Sinn, Franziskus Hauth, Jörg S. Hartig, Zasha Weinberg. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. RNA Biology 2023, 20 (1) , 10-19.
    17. Hubert Salvail, Aparaajita Balaji, Adam Roth, Ronald R. Breaker. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Reports 2023, 42 (12) , 113571.
    18. Conner J Langeberg, Jeffrey S Kieft. A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM. Nucleic Acids Research 2023, 51 (20) , e100-e100.
    19. Dietmar Funck, Malte Sinn, Giuseppe Forlani, Jörg S. Hartig. Guanidine Production by Plant Homoarginine-6-hydroxylases. 2023
    20. Jingdong Xu, Junyuan Hou, Mengnan Ding, Zhiwen Wang, Tao Chen. Riboswitches, from cognition to transformation. Synthetic and Systems Biotechnology 2023, 8 (3) , 357-370.
    21. Caroline M. Focht, David A. Hiller, Sabrina G. Grunseich, Scott A. Strobel. Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity. RNA 2023, 29 (8) , 1126-1139.
    22. Eunho Song, Seungha Hwang, Palinda Ruvan Munasingha, Yeon-Soo Seo, Jin Young Kang, Changwon Kang, Sungchul Hohng. Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination. Nucleic Acids Research 2023, 51 (6) , 2778-2789.
    23. Bryan Banuelos Jara, Ming C. Hammond. Natural Riboswitches. 2023, 1-22.
    24. Bryan Banuelos Jara, Ming C. Hammond. Natural Riboswitches. 2023, 2725-2746.
    25. Madeline E. Sherlock, Gadareth Higgs, Diane Yu, Danielle L. Widner, Neil A. White, Narasimhan Sudarsan, Harini Sadeeshkumar, Kevin R. Perkins, Gayan Mirihana Arachchilage, Sarah N. Malkowski, Christopher G. King, Kimberly A. Harris, Glenn Gaffield, Ruben M. Atilho, Ronald R. Breaker. Architectures and complex functions of tandem riboswitches. RNA Biology 2022, 19 (1) , 1059-1076.
    26. Caroline M Focht, Scott A Strobel. Efficient quantitative monitoring of translational initiation by RelE cleavage. Nucleic Acids Research 2022, 50 (18) , e105-e105.
    27. Franziskus Hauth, Hiltrun Buck, Marco Stanoppi, Jörg S. Hartig. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chemical Biology 2022, 3 (10) , 1240-1250.
    28. Olive E. Burata, Trevor Justin Yeh, Christian B. Macdonald, Randy B. Stockbridge. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. Journal of Biological Chemistry 2022, 298 (10) , 102482.
    29. Akanksha Sharma, Hema Kumari Alajangi, Giuseppina Pisignano, Vikas Sood, Gurpal Singh, Ravi Pratap Barnwal. RNA thermometers and other regulatory elements: Diversity and importance in bacterial pathogenesis. WIREs RNA 2022, 13 (5)
    30. Christin Fuks, Sebastian Falkner, Nadine Schwierz, Martin Hengesbach. Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Frontiers in Molecular Biosciences 2022, 9
    31. D. Funck, M. Sinn, J. R. Fleming, M. Stanoppi, J. Dietrich, R. López-Igual, O. Mayans, J. S. Hartig. Discovery of a Ni2+-dependent guanidine hydrolase in bacteria. Nature 2022, 603 (7901) , 515-521.
    32. Bo Wang, Yao Xu, Xin Wang, Joshua S. Yuan, Carl H. Johnson, Jamey D. Young, Jianping Yu. A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria. Nature Communications 2021, 12 (1)
    33. Sergio Morgado, Érica Fonseca, Ana Carolina Vicente. Genomic epidemiology of rifampicin ADP-ribosyltransferase (Arr) in the Bacteria domain. Scientific Reports 2021, 11 (1)
    34. Robert J. Trachman, Adrian R. Ferré-D'Amaré. An uncommon [K + (Mg 2+ ) 2 ] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. RNA 2021, 27 (10) , 1257-1264.
    35. Jakob Steuer, Oleksandra Kukharenko, Kai Riedmiller, Jörg S Hartig, Christine Peter. Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation. Nucleic Acids Research 2021, 49 (14) , 7954-7965.
    36. Jamie Richards, Joel G. Belasco. Riboswitch control of bacterial RNA stability. Molecular Microbiology 2021, 116 (2) , 361-365.
    37. Malte Sinn, Franziskus Hauth, Felina Lenkeit, Zasha Weinberg, Jörg S. Hartig. Widespread bacterial utilization of guanidine as nitrogen source. Molecular Microbiology 2021, 116 (1) , 200-210.
    38. Claire Husser, Natacha Dentz, Michael Ryckelynck. Structure‐Switching RNAs: From Gene Expression Regulation to Small Molecule Detection. Small Structures 2021, 2 (4)
    39. Zhen Li, Jiayu Gu, Jie Ding, Nanqi Ren, Defeng Xing. Molecular mechanism of ethanol-H2 co-production fermentation in anaerobic acidogenesis: Challenges and perspectives. Biotechnology Advances 2021, 46 , 107679.
    40. Jamie Richards, Joel G. Belasco. Widespread Protection of RNA Cleavage Sites by a Riboswitch Aptamer that Folds as a Compact Obstacle to Scanning by RNase E. Molecular Cell 2021, 81 (1) , 127-138.e4.
    41. Felina Lenkeit, Iris Eckert, Jörg S Hartig, Zasha Weinberg. Discovery and characterization of a fourth class of guanidine riboswitches. Nucleic Acids Research 2020, 48 (22) , 12889-12899.
    42. Carmine J. Slipski, Taylor R. Jamieson, George G. Zhanel, Denice C. Bay, . Riboswitch-Associated Guanidinium-Selective Efflux Pumps Frequently Transmitted on Proteobacterial Plasmids Increase Escherichia coli Biofilm Tolerance to Disinfectants. Journal of Bacteriology 2020, 202 (23)
    43. Jessica A. Brown. Unraveling the structure and biological functions of RNA triple helices. WIREs RNA 2020, 11 (6)
    44. Elizabeth C. Gray, Daniel M. Beringer, Michelle M. Meyer. Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology. Biochemical Society Transactions 2020, 48 (5) , 1941-1951.
    45. Tanisha Teelucksingh, Laura K. Thompson, Georgina Cox, . The Evolutionary Conservation of Escherichia coli Drug Efflux Pumps Supports Physiological Functions. Journal of Bacteriology 2020, 202 (22)
    46. Ronald Micura, Claudia Höbartner. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chemical Society Reviews 2020, 49 (20) , 7331-7353.
    47. Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Michał J. Boniecki, Janusz Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzynska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M. Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA 2020, 26 (8) , 982-995.
    48. Lin Huang, Ting-Wei Liao, Jia Wang, Taekjip Ha, David M J Lilley. Crystal structure and ligand-induced folding of the SAM/SAH riboswitch. Nucleic Acids Research 2020, 78
    49. Madeline E. Sherlock, Ronald R. Breaker. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA 2020, 26 (6) , 675-693.
    50. Shira Stav, Ruben M. Atilho, Gayan Mirihana Arachchilage, Giahoa Nguyen, Gadareth Higgs, Ronald R. Breaker. Genome-wide discovery of structured noncoding RNAs in bacteria. BMC Microbiology 2019, 19 (1)
    51. Huahua Li, Xiaoxue Mei, Bingfeng Liu, Guojun Xie, Nanqi Ren, Defeng Xing. Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition. Biotechnology for Biofuels 2019, 12 (1)
    52. Nikolet Pavlova, Dimitrios Kaloudas, Robert Penchovsky. Riboswitch distribution, structure, and function in bacteria. Gene 2019, 708 , 38-48.
    53. Lin Huang, Jia Wang, Timothy J. Wilson, David M.J. Lilley. Structure-guided design of a high-affinity ligand for a riboswitch. RNA 2019, 25 (4) , 423-430.
    54. Ruben M. Atilho, Kevin R. Perkins, Ronald R. Breaker. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. RNA 2019, 25 (1) , 23-34.
    55. Jordan K. Villa, Yichi Su, Lydia M. Contreras, Ming C. Hammond. Synthetic Biology of Small RNAs and Riboswitches. 2018, 527-545.
    56. Thea S. Lotz, Beatrix Suess. Small-Molecule-Binding Riboswitches. 2018, 75-88.
    57. Robert A. Battaglia, Ailong Ke. Guanidine‐sensing riboswitches: How do they work and what do they regulate?. WIREs RNA 2018, 9 (5)
    58. Lin Huang, David M J Lilley. Structure and ligand binding of the SAM-V riboswitch. Nucleic Acids Research 2018, 46 (13) , 6869-6879.
    59. Thea S. Lotz, Beatrix Suess, , . Small-Molecule-Binding Riboswitches. Microbiology Spectrum 2018, 6 (4)
    60. Jordan K. Villa*, Yichi Su*, Lydia M. Contreras, Ming C. Hammond, , . Synthetic Biology of Small RNAs and Riboswitches. Microbiology Spectrum 2018, 6 (3)
    61. Robert A Battaglia, Ailong Ke. Acting in tandem. eLife 2018, 7
    62. Ali A. Kermani, Christian B. Macdonald, Roja Gundepudi, Randy B. Stockbridge. Guanidinium export is the primal function of SMR family transporters. Proceedings of the National Academy of Sciences 2018, 115 (12) , 3060-3065.
    63. Gayan Mirihana Arachchilage, Madeline E. Sherlock, Zasha Weinberg, Ronald R. Breaker. SAM-VI RNAs selectively bind S -adenosylmethionine and exhibit similarities to SAM-III riboswitches. RNA Biology 2018, 15 (3) , 371-378.
    64. Etienne B. Greenlee, Shira Stav, Ruben M. Atilho, Kenneth I. Brewer, Kimberly A. Harris, Sarah N. Malkowski, Gayan Mirihana Arachchilage, Kevin R. Perkins, Madeline E. Sherlock, Ronald R. Breaker. Challenges of ligand identification for the second wave of orphan riboswitch candidates. RNA Biology 2018, 15 (3) , 377-390.
    65. Lin Huang, Jia Wang, Timothy J. Wilson, David M.J. Lilley. Structure of the Guanidine III Riboswitch. Cell Chemical Biology 2017, 24 (11) , 1407-1415.e2.
    66. Zasha Weinberg, Christina E. Lünse, Keith A. Corbino, Tyler D. Ames, James W. Nelson, Adam Roth, Kevin R. Perkins, Madeline E. Sherlock, Ronald R. Breaker. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Research 2017, 45 (18) , 10811-10823.
    67. Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang. Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches. Molecules 2017, 22 (7) , 1169.
    68. Phillip J. McCown, Keith A. Corbino, Shira Stav, Madeline E. Sherlock, Ronald R. Breaker. Riboswitch diversity and distribution. RNA 2017, 23 (7) , 995-1011.
    69. Lin Huang, Jia Wang, David M.J. Lilley. The Structure of the Guanidine-II Riboswitch. Cell Chemical Biology 2017, 24 (6) , 695-702.e2.
    70. Christopher P. Jones, Adrian R. Ferré-D'Amaré. Long-Range Interactions in Riboswitch Control of Gene Expression. Annual Review of Biophysics 2017, 46 (1) , 455-481.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect