@article {31,
	title = {Derepression of INO1 transcription requires cooperation between the Ino2p-Ino4p heterodimer and Cbf1p and recruitment of the ISW2 chromatin-remodeling complex.},
	journal = {Eukaryot Cell},
	volume = {9},
	year = {2010},
	month = {2010 Dec},
	pages = {1845-55},
	abstract = {<p>The Saccharomyces cerevisiae INO1 gene encodes the structural enzyme inositol-3-phosphate synthase for the synthesis de novo of inositol and inositol-containing phospholipids. The transcription of INO1 is completely derepressed in the absence of inositol and choline (I(-) C(-)). Derepression requires the binding of the Ino2p-Ino4p basic helix-loop-helix (bHLH) heterodimer to the UAS(INO) promoter element. We report here the requirement of a third bHLH protein, centromere-binding factor 1 (Cbf1p), for the complete derepression of INO1 transcription. We found that Cbf1p regulates INO1 transcription by binding to sites distal to the INO1 promoter and encompassing the upstream SNA3 open reading frame (ORF) and promoter. The binding of Cbf1p requires Ino2p-Ino4p binding to the UAS(INO) sites in the INO1 promoter and vice versa, suggesting a cooperative mechanism. Furthermore, Cbf1p binding to the upstream sites was required for the binding of the ISW2 chromatin-remodeling complex to the Ino2p-Ino4p-binding sites on the INO1 promoter. Consistent with this, ISW2 was also required for the complete derepression of INO1 transcription.</p>
},
	keywords = {Adenosine Triphosphatases, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Basic Helix-Loop-Helix Transcription Factors, Chromatin, Chromatin Assembly and Disassembly, Dimerization, Gene Expression Regulation, Fungal, Myo-Inositol-1-Phosphate Synthase, Promoter Regions, Genetic, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic},
	issn = {1535-9786},
	doi = {10.1128/EC.00144-10},
	author = {Shetty, Ameet and Lopes, John M}
}
@article {395,
	title = {A degenerate tripartite DNA-binding site required for activation of ComA-dependent quorum response gene expression in Bacillus subtilis.},
	journal = {J Mol Biol},
	volume = {381},
	year = {2008},
	month = {2008 Aug 29},
	pages = {261-75},
	abstract = {In Bacillus subtilis, the transcription factor ComA activates several biological processes in response to increasing population density. Extracellular peptide signaling is used to coordinate the activity of ComA with population density. At low culture densities, when the concentration of signaling peptides is lowest, ComA is largely inactive. At higher densities, when the concentration of signaling peptides is higher, ComA is active and activates the transcription of at least nine operons involved in the development of competence and in the production of degradative enzymes and antibiotics. We found that ComA binds a degenerate tripartite sequence consisting of three DNA-binding determinants or "recognition elements." Mutational analyses showed that all three recognition elements are required for transcription activation in vivo and for specific DNA binding by ComA in vitro. Degeneracy of the recognition elements in the ComA-binding site is an important regulatory feature for coordinating transcription with population density (i.e., promoters containing an optimized binding site have high activity at low culture density and are no longer regulated in the normal-density-dependent manner). We found that purified ComA forms a dimer in solution, and we propose a model for how two dimers of ComA bind to an odd number of DNA-binding determinants to activate transcription of target genes. This DNA-protein architecture for transcription activation appears to be conserved for ComA homologs in other Bacillus species.},
	keywords = {Bacillus subtilis, Bacterial Proteins, Base Sequence, Binding Sites, Dimerization, DNA, Bacterial, DNA-Binding Proteins, Electrophoretic Mobility Shift Assay, Gene Expression Regulation, Bacterial, Peptide Synthases, Phosphoprotein Phosphatases, Promoter Regions, Genetic, Protein Binding, Quorum Sensing, Sequence Analysis, DNA, Transcription, Genetic, Transcriptional Activation},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2008.06.035},
	author = {Griffith, Kevin L and Grossman, Alan D}
}
@article {826,
	title = {Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {98},
	year = {2001},
	month = {2001 Jul 17},
	pages = {8203-10},
	abstract = {Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec(-) and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4{\textquoteright},6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16\% of the cells were filamented and had poorly partitioned chromosomes (Par(-)). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par(-) phenotype. Filamentation in the recB mutant decreased to 3\%, but increased to 28\% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1cat was lethal with priA2kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.},
	keywords = {Adenosine Triphosphatases, Bacterial Proteins, Cell Division, Chromosomes, Bacterial, Dimerization, DNA Helicases, Endodeoxyribonucleases, Escherichia coli, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Gene Expression, Membrane Proteins, Mutagenesis, Rec A Recombinases, Recombination, Genetic, SOS Response (Genetics)},
	issn = {0027-8424},
	doi = {10.1073/pnas.121007698},
	author = {McCool, J D and Sandler, S J}
}
