Robert W. and Estelle S. Bingham Professor of Biological Sciences
Ph.D. Univ. of Wisconsin, 1984
Postdoc. Tufts Univ. School of Medicine, 1984-1987
The main area of interest in our laboratory is the analysis of the mechanisms through which cells sense changes in their environment and transmit that information to the level of gene expression.We use the Gram-positive bacterium Bacillus subtilis as a model system, and we focus primarily on genes involved in protein synthesis and amino acid metabolism.We have uncovered systems in which nascent RNA transcripts act as riboswitches to directly sense physiological signals and control gene expression through RNA structural rearrangements.
Nascent RNAs can sense uncharged tRNA: the T box riboswitch
Characterization of the B. subtilis tyrS gene, encoding tyrosyl-tRNA synthetase, revealed a novel mechanism of gene regulation at the level of transcription antitermination. The tyrSgene is a member of a large family of aminoacyl-tRNA synthetase and amino acid biosynthesis genes in Gram-positive bacteria that are regulated by a common mechanism.Each gene in this family responds individually to limitation for the appropriate amino acid. Amino acid limitation is monitored via interaction of the 5’ region of the nascent transcript with the cognate uncharged tRNA.This interaction is directed by pairing of the anticodon of the tRNA with a single codon, designated the "Specifier Sequence," in the mRNA.The mRNA-tRNA interaction occurs in the absence of translation, and antitermination can occur in a purified transcription system with no additional cellular factors, indicating that the mRNA is sufficient for specific recognition of the cognate tRNA.We are currently investigating the molecular details of the leader RNA-tRNA interaction, and the structural shifts in both RNA partners that occur upon binding.We are also testing novel antibiotics for their ability to target the T box mechanism.
Nascent RNAs can sense small molecules: metabolite-binding riboswitch RNAs
Analysis of genes involved in methionine metabolism revealed a second global transcription antitermination system, dedicated to genes in this pathway.Like the T box system, the S box system is widely used in Gram-positive organisms. Genes regulated by this mechanism contain highly conserved sequence and structural elements in their mRNAs, and expression is induced by starvation for methionine. We have now shown that the molecular effector for this system is S–adenosylmethionine (SAM), which binds directly to the leader RNA and modulates its structure to promote transcription termination. A second SAM-binding RNA, the SMK box, was identified in lactic acid bacteria and shown to regulate gene expression at the level of translation initiation.We have also shown that lysine biosynthesis genes are regulated by a similar mechanism, with specific leader RNA binding of lysine.Current work is focusing on the molecular mechanisms of effector recognition and RNA rearrangement in response to effector binding.
- Wilson Mitchell SN, Grundy FJ & Henkin TM. (2012) Analysis of Lysine recognition and specificity of the Bacillus subtilis L box riboswitch. Nucl. Acids Res., in press.
- Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM & Ke A. (2011) Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J. Mol. Biol. 409, 786-799.
- Wilson RC, Smith AM, Fuchs RT, Kleckner IR, Henkin TM & Foster MP. (2011) Tuning riboswitch regulation through conformational selection. J Mol Biol. 405, 926-938.
- Smith AM, Fuchs RT, Grundy FJ & Henkin TM. (2010) The SMK box of Enterococcus faecalis is a reversible riboswitch. Mol Microbiol. 78,1393-1402.
- Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes MW, Henkin TM & Ke A. (2010) SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S Box/SAM-I riboswitch. J Mol Biol. 404, 803-818.
- Wang J, Henkin TM & Nikonowicz EP. (2010) NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA. Nucl. Acids Res. 38, 3388-3398.
- Smith AM, Fuchs RT & Henkin TM. (2010) Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal. RNA Biol. 7, 104-110.
- Johnson CM, Manias DA, Haemig HA, Shokeen S, Weaver KE, Henkin TM & Dunny GA. (2010) Direct evidence for control of the pheromone prgQ operon of Enterococcus faecalis plasmid pCF10 by a countertranscript-driven attenuation mechanism. J Bacteriol. 192, 1634-1642.
- Green NR, Grundy FJ & Henkin TM. (2010) The T box mechanism: tRNA as a regulatory molecule. FEBS Lett. 584,318-24.
- Gutierrez-Preciado A, Henkin TM, Grundy FJ, Yanofsky C & Merino E. (2009) Biochemical features and functional implications of the RNA-based T box regulatory mechanism. Microbiol Mol Biol Rev. 73, 36-61.
- Henkin TM. (2008) Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev. 22, 3383-90.
- Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar F, Henkin TM & Ke A. (2008) Crystal structures of the SMK box riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat Struct Mol Biol. 15, 1076-83.
- Ontiveros-Palacios A, Smith AM, Grundy FJ, Soberon M, Henkin TM & Miranda-Rios J. (2008) Molecular basis for thiamin pyrophosphate recognition and gene regulation by the THI-box riboswitch. Mol Microbiol. 67, 793-803.
- Tomsic J, McDaniel BA, Grundy FJ & Henkin TM. (2008) Natural variability in SAM-dependent riboswitches: S box elements in Bacillus subtilis exhibit differential sensitivity to SAM in vivo and in vitro. J Bacteriol. 190, 823-33.
- Fuchs RT, Grundy FJ & Henkin TM. (2007) S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box riboswitch RNA. Proc Natl Acad Sci U S A. 104, 4876-80.
- Fuchs RT, Grundy FJ & Henkin TM. (2006) The SMK box is a new SAM binding RNA element that regulates translation of bacterial SAM synthetase genes. Nat Struct Mol Biol. 13, 226-33.
- Grundy FJ, Yousef MR & Henkin TM. (2005) Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene. J Mol Biol. 346, 73-81.
Snyder LR, Peters JE, Henkin TM & Champness WC. (2012) Molecular Genetics of Bacteria, 4th Edition. American Society for Microbiology, Washington, DC, in press.
The all-time favorite:
- Grundy FJ & Henkin TM. (1993) tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell. 74, 475-82.