Biochemical validation of a second guanidine riboswitch class in bacteria

Biochemistry

Volumn 56, Issue 2, 2017, Pages 352-358

  Sherlock, Madeline E ^a   Malkowski, Sarah N ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; GENES; LIGANDS; PROTEINS; RNA; SIGNAL ENCODING;

COMPARATIVE GENOMIC; GENE ASSOCIATIONS; GENES ENCODING; PROTEIN FACTORS; RIBOSWITCHES; RNA STRUCTURES; STEM-LOOP STRUCTURES; TOXIC EFFECT;

ENCODING (SYMBOLS);

BACTERIAL PROTEIN; BACTERIAL RNA; CARBOXYLASE; EMRE PROTEIN; GUANIDINE; LIGAND; MINI YKKC RNA; SUGE PROTEIN; UNCLASSIFIED DRUG; ANTIPORTER; APTAMER; EMRE PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; GUANIDINE DERIVATIVE; RIBOSWITCH;

ARTICLE; BACTERIUM; BIOCHEMICAL ANALYSIS; COMPARATIVE STUDY; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENETIC ANALYSIS; NONHUMAN; NUCLEOTIDE MOTIF; PRIORITY JOURNAL; RIBOSWITCH; RNA STRUCTURE; RNA-BINDING DOMAIN; VALIDATION STUDY; BIOLOGY; CHEMISTRY; CONFORMATION; CYANOBACTERIUM; DRUG EFFECTS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; KLEBSIELLA PNEUMONIAE; METABOLISM;

ANTIPORTERS; APTAMERS, NUCLEOTIDE; COMPUTATIONAL BIOLOGY; CYANOBACTERIA; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GUANIDINES; KLEBSIELLA PNEUMONIAE; LIGANDS; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA, BACTERIAL;

EID: 85019668463     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.6b01270     Document Type: Article

References (17)

1. Barrick, J. E., Corbino, K. A., Winkler, W. C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J. K., and Breaker, R. R. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A. 101, 6421-6426.
2. Meyer, M. M., Hammond, M. C., Salinas, Y., Roth, A., Sudarsan, N., and Breaker, R. R. (2011) Challenges of ligand identification for riboswitch candidates. RNA Biol. 8, 5-10.
3. Weinberg, Z., Barrick, J. E., Yao, Z., Roth, A., Kim, J. N., Gore, J., et al. (2007) Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 35, 4809-4819.
4. Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., and Breaker, R. R. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol. 11, R31.
5. Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B., and Breaker, R. R. (2017) Metabolism of free guanidine in bacteria is regulated by a widespread riboswitch class. Mol. Cell 65, 1-11.
6. Sherlock, M. E., and Breaker, R. R. (2017) Biochemical validation of a third guanidine riboswitch class in bacteria. Biochemistry, DOI: 10.1021/acs.biochem.6b01271.
7. Nawrocki, E. P., and Eddy, S. R. (2013) Infernal 1.1:100-fold faster RNA homology searches. Bioinformatics 29, 2933-2935.
8. Weinberg, Z., Kim, P. B., Chen, T. H., Li, S., Harris, K. A., Lunse, C. E., and Breaker, R. R. (2015) New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat. Chem. Biol. 11, 606-610.
9. Weinberg, Z., and Breaker, R. R. (2011) R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinf. 12, 3.
10. Regulski, E. E., and Breaker, R. R. (2008) In-line probing analysis of riboswitches. Methods Mol. Biol. 419, 53-67.
11. Soukup, G. A., and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5, 1308-1325.
12. Schuldin'er, S. S. (2009) EmrE, a model for studying evolution and mechanism of ion-coupled transporters. Biochim. Biophys. Acta, Proteins Proteomics 1794, 748-762.
13. Reiss, C. W., Xiong, Y., and Strobel, S. A. (2017) Structural basis for ligand binding to the ykkC guanidine riboswitch. Structure, DOI: 10.1016/j.str.2016.11.020.
14. 1 contains an unusually small aptamer domain. Nat. Struct. Mol. Biol. 14, 308-317.
15. 1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat. Struct. Mol. Biol. 16, 343-344.
16. 0 metabolite by an unusually small riboswitch aptamer domain. J. Biol. Chem. 284, 11012-11016.
17. Ruff, K. M., Muhammad, A., McCown, P. J., Breaker, R. R., and Strobel, S. A. (2016) Singlet glycine riboswitches bind ligand as well as tandem riboswitches. RNA 22, 1728-1738.