T box sequences have
been identified upstream of a large number of uncharacterized genes such as
transporters in bacterial genomes. Expression of each T box family gene is
induced by limitation for a specific amino acid. T box family genes contain an
untranslated leader region containing a factor-independent transcriptional
terminator upstream of the structural genes. The anticodon of uncharged tRNA
base-pairs with the leader mRNA at a codon referred to as the specifier sequence,
inducing formation of an alternative antiterminator structure, allowing
expression of the structural genes. There
are several additional conserved primary sequence and secondary structural
elements. Analysis of these elements can be used to predict the identity of the
specifier codon and the amino acid signal. Bacillus subtilishypothetical
amino acid permease, yvbW, was analyzed
as an example of this type of transcriptional regulatory prediction suggesting expression
in response to leucine limitation. Expression was induced up to 130-fold in
response to leucine limitation, utilizing a yvbW-lacZ transcriptional fusion. These data suggest that hypothetical amino acid
permease YvbW may participate in leucine metabolism. A yvbW knockout strain was generated, although the substrate
specificity for the putative amino acid permease was not identified.
Gutiérrez-Preciado, A., Henkin, T.M., Grundy, F.J., Yanofsky, C. and Merino, E. (2009) Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism. Microbiology and Molecular Biology Reviews, 73, 36-61. http://dx.doi.org/10.1128/MMBR.00026-08
Grundy, F.J., Rollins, S.M. and Henkin, T.M. (1994) Interaction between the Acceptor end of tRNA and the T Box Stimulates Antitermination in the Bacillus subtilis tyrS Gene: A New Role for the Discriminator Base. Journal of Bacteriology, 176, 4518-4526.
Grigg, J.C., Chen, Y., Grundy, F.J., Henkin, T.M., Pollack, L. and Ke, A. (2013) T Box RNA Decodes both the Information Content and Geometry of tRNA to Affect Gene Expression. Proceedings of the National Academy of Sciences of the United States of America, 110, 7240-7245. http://dx.doi.org/10.1073/pnas.1222214110
Rollins, S.M., Grundy, F.J. and Henkin, T.M. (1997) Analysis of cis-Acting Sequence and Structural Elements Required for Antitermination of the Bacillus subtilis tyrS Gene. Molecular Microbiology, 25, 411-421.
Winkler, W.C., Grundy, F.J., Murphy, B.A. and Henkin, T.M. (2001) The GA Motif: An RNA Element Common to Bacterial Antitermination Systems, rRNA, and Eukaryotic RNAs. RNA, 7, 1165-1172.
Putzer, H., Gendron, N. and Grunberg-Manago, M. (1992) Coordinate Expression of the Two Threonyl-tRNA Synthetase Genes in Bacillus subtilis: Control by Transcriptional Antitermination Involving a Conserved Regulatory Sequence. The EMBO Journal, 11, 3117-3127.
Saad, N.Y., Stamatopoulou, V., Brayé, M., Drainas, D., Stathopoulos, C. and Becker, H.D. (2013) Two-Codon T-Box Riboswitch Binding Two tRNAs. Proceedings of the National Academy of Sciences of the United States of America, 110, 12756-127561. http://dx.doi.org/10.1073/pnas.1304307110
Wels, M., Groot Kormelink, T., Kleerebezem, M., Siezen, R.J. and Francke, C. (2008) An in Silico Analysis of T-Box Regulated Genes and T-Box Evolution in Prokaryotes, with Emphasis on Prediction of Substrate Specificity of Transporters. BMC Genomics, 9, 330. http://dx.doi.org/10.1186/1471-2164-9-330
Henkin, T.M., Glass, B.L. and Grundy, F.J. (1992) Analysis of the Bacillus subtilis tyrS Gene: Conservation of a Regulatory Sequence in Multiple tRNA Synthetase Genes. Journal of Bacteriology, 174, 1299-1306.
Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meurice, G., Sekowska, A., Vallenet, D., Wang, T., Moszer, I., Médigue, C. and Danchin, A. (2009) From a Consortium Sequence to a Unified Sequence: The Bacillus subtilis 168 Reference Genome a Decade Later. Microbiology, 155, 1758-1775. http://dx.doi.org/10.1099/mic.0.027839-0
Steinmetz, M. and Richter, R. (1994) Plasmids Designed to Alter the Antibiotic Resistance Expressed by Insertion Mutations in Bacillus subtilis, through in Vivo Recombination. Gene, 142, 79-83.
Wang, J., Henkin, T.M. and Nikonowicz, E.P. (2010) NMR Structure and Dynamics of the Specifier Loop Domain from the Bacillus subtilis tyrS T Box Leader RNA. Nucleic Acids Research, 38, 3388-3398.
Belitsky, B.R., Gustafsson, M.C.U., Sonenshein, A.L. and Von Wachenfeldt, C. (1997) An lrp-Like Gene of Bacillus subtilis Involved in Branched-Chain Amino Acid Transport. Journal of Bacteriology, 179, 5448-5457.
Rasmussen, S., Nielsen, H.B. and Jarmer, H. (2009) The Transcriptionally Active Regions in the Genome of Bacillus subtilis. Molecular Microbiology, 73, 1043-1057. http://dx.doi.org/10.1111/j.1365-2958.2009.06830.x
Chopin, A., Biaudet, V. and Ehrlich, S.D. (1998) Analysis of the Bacillus subtilis Genome Sequence Reveals Nine New T-Box Leaders. Molecular Microbiology, 29, 662-664. http://dx.doi.org/10.1046/j.1365-2958.1998.00912.x
Wray, L.V., Ferson, A.E., Rohrer, K. and Fisher, S.H. (1996) TnrA, a Transcription Factor Required for Global Nitrogen Regulation in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America, 93, 8841-8845. http://dx.doi.org/10.1073/pnas.93.17.8841
Brechtel, C.E. and King, S.C. (1998) 4-Aminobutyrate (GABA) Transporters from the Amine-Polyamine-Choline Superfamily: Substrate Specificity and Ligand Recognition Profile of the 4-Aminobutyrate Permease from Bacillus subtilis. Biochemical Journal, 333, 565-571.