The ability of a cell to function normally and carry out its specialized functions depends critically on the proper regulation and expression of its genes. This regulation has its roots in the diversity and specificity of interactions between biological macromolecules. At the level of control of transcription this means primarily the interactions between promoter DNA sequences and proteins and the interactions of proteins with each other. We study how these interactions occur and what they do to control the process of gene transcription. We also study what is wrong with these interactions when mutations cause defects in transcription and how certain effectors might influence the expression of the mutant and normal genes.

The approach used relies on comparing transcriptional control in reconstructed systems with that occurring inside cells. We have developed chemistry-based procedures for probing the interactions of proteins with DNA. These are applied to mammalian, yeast and bacterial cells and extracts under conditions where the activity of genes may be controlled by biological means. The results lead to models for what types of nucleoprotein complexes assemble when genes are active and how this changes when they are inactivated by mutation or by biological repression. These models are tested by isolating the regulatory macromolecules from cells and reconstructing the system in vitro. In some cases the isolated proteins are then mutated to learn the roles of specific protein domains in transcriptional regulation. The picture that is emerging promises to contribute significantly to our understanding of what goes wrong when cells specify inappropriate patterns of gene transcription and are converted to the transformed state.

Gralla Group Publications from 1995 - 1999

Gralla Group Publications from 2000 - Present

Adam Z. Rosenthal, Youngbae Kim and Jay D. Gralla (2008) Regulation of transcription by acetate in E. coli: In vitro and in vivo comparisons. Mol. Micro. In press.

Adam Z. Rosenthal, Youngbae Kim and Jay D. Gralla (2008) Poising of Escherichia coli RNA Polymerase and its release from the σ38 C-Terminal Tail for osmY Transcription. J. Mol. Biol. 376:938-949.

Youngbae Kim, Chih M. Lew, and Jay D. Gralla (2006) E. coli pfs transcription: regulation and proposed roles in autoinducer-2 synthesis and purine excretion. J. Bact. 188:7457-63.

Jay D. Gralla and David R. Vargas (2006) Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation. Embo J. 25:1515-21.

Adam Z. Rosenthal, Minshan Hu and Jay D. Gralla (2006) Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS). Mol. Micro. 59:1052-6.

Yin C. Lin and Jay D. Gralla (2005) Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE. Nuc. Acids Res. 33:3072-8.

Yin C. Lin, Wai S. Choi and Jay D Gralla (2005) TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nature Structural and Molecular Biology, 12:603-07.

Jay D. Gralla (2005) E. coli ribosomal RNA transcription: Regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Micro. 55:973-977.

Chih Lew and Jay D. Gralla (2004) Nucleotide dependent isomerization of E. coli RNA polymerase. Biochemistry, 43:2660-6.

Wai S. Choi, Yin C. Lin and Jay D. Gralla (2004) The Schizosaccharomyces pombe open promoter bubble: Mammalian-like arrangement and properties. J. Mol. Biol. 340:981-9

Chih Lew and Jay D. Gralla (2004) Mechanism of stimulation of ribosomal promoters by the +1 and +2 nucleotides. J Biol Chem, 279:19481-5.

Shun Lee and Jay D. Gralla (2004) Osomoregulation of bacterial transcription via poised RNA polymerase. Mol. Cell, 14:153-62

Lin YC, Choi WS and Gralla JD. (2005) TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nat Struct Mol Biol. 12, 603-7.

Lin YC and Gralla JD. (2005) Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE. Nucleic Acids Res. 33, 3072-81.

Gralla JD. (2005) Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol. 55, 973-7.

Lew CM and Gralla JD. (2004) Nucleotide-dependent isomerization of Escherichia coli RNA polymerase. Biochemistry 43,12660-6.

Choi WS, Lin YC and Gralla JD. (2004) The Schizosaccharomyces pombe open promoter bubble: mammalian-like arrangement and properties. J Mol Biol. 340, 981-9.

Lew CM and Gralla JD. (2004) Mechanism of stimulation of ribosomal promoters by binding of the +1 and +2 nucleotides. J Biol Chem. 279,19481-5.

Lee SJ and Gralla JD. (2004) Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol Cell. 14, 153-62.

Fenton M and Gralla JD. (2003) Roles for inhibitory interactions in the use of the - 10 promoter element by sigma 70 holoenzyme. J Biol Chem. 278, 39669-39674.

Fenton M and Gralla JD. (2003) Effect of DNA bases and backbone on sigma70 holoenzyme binding and isomerization using fork junction probes. Nuc. Acids Res. 31, 2745-2750.

Lee SL and Gralla JD. (2003) Open Complex Formation in vitro by Sigma38 (rpoS) RNA Polymerase: Roles for Region 2 Amino Acids J. Mol. Biol. 329, 941-8

Lee SL and Gralla JD. (2002) Promoter use by sigma38 (rpoS) RNA polymerase: amino acid clusters for DNA binding and isomerization. J. Biol. Chem. 277, 47420-47427.

Lew C and Gralla JD. (2002) New roles for conserved domains within a sigma54 dependent binding protein. J. Biol. Chem. 277, 41517-41524.

Choi WS, Yan M, Nusinow D and Gralla JD. (2002) In vitro Transcription and Start Site selection in S. Pombe. J. Mol. Biol. 319, 1005-1013.

Lee SJ and Gralla JD. (2001), Sigma38 (rpoS) RNA polymerase promoter engagement via –10 region nucleotides, J. Biol. Chem 276, 30064-30071.

Fenton M and Gralla JD. (2001), Function of the bacterial TATAAT element as single stranded DNA during RNA polymerase isomerization, PNAS 98, 9020-9025.

Wang L and Gralla JD. (2001) Roles for the C-terminal region of Sigma 54 in transcriptional silencing and DNA-binding, J. Biol. Chem. 276, 8979-8986.

Wolner B and Gralla JD. (2001) TATA-flanking sequences influence the rate and stability of TBP and TFIIB binding, J. Biol. Chem. 276, 6260-6266.

Guo Y, Lew CM and Gralla JD. (2000) Promoter opening by sigma 54 and sigma 70 RNA polymerases: sigma factor-directed alterations in the mechanism and tightness of control. Genes & Dev. 14, 2242-2255.

Gralla JD. (2000), Signaling through Sigma, Nature Stuctural Biology 7, 530-532.

Buck M, Gallegos M, Studholme DJ, Guo Y and Gralla JD. (2000) The bacterial enhancer dependent s54 (sN) transcription factor. J. Bact. 182, 4129-4136.

Wolner B and Gralla JD. (2000) Roles For Non-TATA Core Promoter Sequences In Transcription and Factor Binding. Mol. Cell. Biol. 20, 3608-3615.

Fenton M, Lee SJ and Gralla JD (2000) E. coli promoter opening and -10 recognition: mutational analysis of sigma 70. EMBO J 19, 1130-1137.