@article {1562,
	title = {Regulation of ethanol-related behavior and ethanol metabolism by the Corazonin neurons and Corazonin receptor in Drosophila melanogaster.},
	journal = {PLoS One},
	volume = {9},
	year = {2014},
	month = {2014},
	pages = {e87062},
	abstract = {<p>Impaired ethanol metabolism can lead to various alcohol-related health problems. Key enzymes in ethanol metabolism are alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH); however, neuroendocrine pathways that regulate the activities of these enzymes are largely unexplored. Here we identified a neuroendocrine system involving Corazonin (Crz) neuropeptide and its receptor (CrzR) as important physiological regulators of ethanol metabolism in Drosophila. Crz-cell deficient (Crz-CD) flies displayed significantly delayed recovery from ethanol-induced sedation that we refer to as hangover-like phenotype. Newly generated mutant lacking Crz Receptor (CrzR(01) ) and CrzR-knockdown flies showed even more severe hangover-like phenotype, which is causally associated with fast accumulation of acetaldehyde in the CrzR(01) mutant following ethanol exposure. Higher levels of acetaldehyde are likely due to 30\% reduced ALDH activity in the mutants. Moreover, increased ADH activity was found in the CrzR(01) mutant, but not in the Crz-CD flies. Quantitative RT-PCR revealed transcriptional upregulation of Adh gene in the CrzR(01) . Transgenic inhibition of cyclic AMP-dependent protein kinase (PKA) also results in significantly increased ADH activity and Adh mRNA levels, indicating PKA-dependent transcriptional regulation of Adh by CrzR. Furthermore, inhibition of PKA or cAMP response element binding protein (CREB) in CrzR cells leads to comparable hangover-like phenotype to the CrzR(01) mutant. These findings suggest that CrzR-associated signaling pathway is critical for ethanol detoxification via Crz-dependent regulation of ALDH activity and Crz-independent transcriptional regulation of ADH. Our study provides new insights into the neuroendocrine-associated ethanol-related behavior and metabolism.</p>},
	keywords = {Acetaldehyde, Alcohol Dehydrogenase, Aldehyde Dehydrogenase, Alleles, Animals, Cyclic AMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Ethanol, Genes, Reporter, Male, Mutation, Neurons, Neuropeptides, Phenotype, Receptors, Neuropeptide, RNA, Messenger, Transcription, Genetic},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0087062},
	author = {Sha, Kai and Choi, Seung-Hoon and Im, Jeongdae and Lee, Gyunghee G and Loeffler, Frank and Park, Jae H}
}
@article {1456,
	title = {Saccharomyces cerevisiae essential genes with an Opi- phenotype.},
	journal = {G3 (Bethesda)},
	volume = {4},
	year = {2014},
	month = {2014 Apr},
	pages = {761-7},
	abstract = {<p>The overproduction and secretion of inositol (i.e., Opi(-)) phenotype is associated with defects in regulation of phospholipid biosynthesis in yeast. Here we report a screen of the essential yeast gene set using a conditional-expression library. This screen identified novel functions previously unknown to affect phospholipid synthesis.</p>
},
	keywords = {Cluster Analysis, Genes, Essential, Histone Acetyltransferases, Inositol, Phenotype, Phospholipids, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins},
	issn = {2160-1836},
	doi = {10.1534/g3.113.010140},
	author = {Salas-Santiago, Bryan and Lopes, John M}
}
@article {466,
	title = {Genome-scale constraint-based modeling of Geobacter metallireducens.},
	journal = {BMC Syst Biol},
	volume = {3},
	year = {2009},
	month = {2009},
	pages = {15},
	abstract = {BACKGROUND: Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens.

RESULTS: The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens{\textquoteright} specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome-scale metabolic model, which provided a fast and cost-effective way to understand the metabolism of G. metallireducens.

CONCLUSION: We have developed a genome-scale metabolic model for G. metallireducens that features both metabolic similarities and differences to the published model for its close relative, G. sulfurreducens. Together these metabolic models provide an important resource for improving strategies on bioremediation and bioenergy generation.},
	keywords = {Biodegradation, Environmental, Biomass, Computer Simulation, Ecosystem, Electron Transport, Energy Metabolism, Genome, Bacterial, Geobacter, Iron, Metabolic Networks and Pathways, Models, Biological, Models, Genetic, Mutation, Phenotype, Species Specificity, Systems Biology},
	issn = {1752-0509},
	doi = {10.1186/1752-0509-3-15},
	author = {Sun, Jun and Sayyar, Bahareh and Butler, Jessica E and Pharkya, Priti and Fahland, Tom R and Famili, Iman and Schilling, Christophe H and Lovley, Derek R and Mahadevan, Radhakrishnan}
}
@article {484,
	title = {Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation.},
	journal = {Int J Syst Evol Microbiol},
	volume = {58},
	year = {2008},
	month = {2008 May},
	pages = {1075-8},
	abstract = {A Gram-negative, rod-shaped, motile bacterium, strain Rf4T, which conserves energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation, was isolated from subsurface sediment undergoing uranium bioremediation. The 16S rRNA gene sequence of strain Rf4T matched sequences recovered in 16S rRNA gene clone libraries constructed from DNA extracted from groundwater sampled at the same time as the source sediment. Cells of strain Rf4T were regular, motile rods, 1.2-2.0 microm long and 0.5-0.6 microm in diameter, with rounded ends. Cells had one lateral flagellum. Growth was optimal at pH 6.5-7.0 and 32 degrees C. With acetate as the electron donor, strain Rf4T used Fe(III), Mn(IV), anthraquinone-2,6-disulfonate, malate and fumarate as electron acceptors and reduced U(VI) in cell suspensions. With poorly crystalline Fe(III) oxide as the electron acceptor, strain Rf4T oxidized the following electron donors: acetate, lactate, pyruvate and ethanol. Phylogenetic analysis of the 16S rRNA gene sequence of strain Rf4T placed it in the genus Geobacter. Strain Rf4T was most closely related to {\textquoteright}Geobacter humireducens{\textquoteright} JW3 (95.9 \% sequence similarity), Geobacter bremensis Dfr1T (95.4 \%) and Geobacter bemidjiensis BemT (95.1 \%). Based on phylogenetic analysis and phenotypic differences between strain Rf4T and closely related Geobacter species, this strain is described as a representative of a novel species, Geobacter uraniireducens sp. nov. The type strain is Rf4T (=ATCC BAA-1134T =JCM 13001T).},
	keywords = {Bacterial Typing Techniques, DNA, Bacterial, Genes, rRNA, Genotype, Geobacter, Geologic Sediments, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species Specificity, Uranium},
	issn = {1466-5026},
	doi = {10.1099/ijs.0.65377-0},
	author = {Shelobolina, Evgenya S and Vrionis, Helen A and Findlay, Robert H and Lovley, Derek R}
}
@article {524,
	title = {Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.},
	journal = {Appl Environ Microbiol},
	volume = {72},
	year = {2006},
	month = {2006 Feb},
	pages = {1558-68},
	abstract = {Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttle-producing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.},
	keywords = {Amino Acids, Electron Transport, Escherichia coli, Fumarates, Geobacter, Iron, Models, Biological, Mutation, Oxidation-Reduction, Phenotype, Protons, Quinones, Species Specificity},
	issn = {0099-2240},
	doi = {10.1128/AEM.72.2.1558-1568.2006},
	author = {Mahadevan, R and Bond, D R and Butler, J E and Esteve-Nu{\~n}ez, A and Coppi, M V and Palsson, B O and Schilling, C H and Lovley, D R}
}
@article {37,
	title = {Genomic analysis of the Opi- phenotype.},
	journal = {Genetics},
	volume = {173},
	year = {2006},
	month = {2006 Jun},
	pages = {621-34},
	abstract = {Most of the phospholipid biosynthetic genes of Saccharomyces cerevisiae are coordinately regulated in response to inositol and choline. Inositol affects the intracellular levels of phosphatidic acid (PA). Opi1p is a repressor of the phospholipid biosynthetic genes and specifically binds PA in the endoplasmic reticulum. In the presence of inositol, PA levels decrease, releasing Opi1p into the nucleus where it represses transcription. The opi1 mutant overproduces and excretes inositol into the growth medium in the absence of inositol and choline (Opi(-) phenotype). To better understand the mechanism of Opi1p repression, the viable yeast deletion set was screened to identify Opi(-) mutants. In total, 89 Opi(-) mutants were identified, of which 7 were previously known to have the Opi(-) phenotype. The Opi(-) mutant collection included genes with roles in phospholipid biosynthesis, transcription, protein processing/synthesis, and protein trafficking. Included in this set were all nonessential components of the NuA4 HAT complex and six proteins in the Rpd3p-Sin3p HDAC complex. It has previously been shown that defects in phosphatidylcholine synthesis (cho2 and opi3) yield the Opi(-) phenotype because of a buildup of PA. However, in this case the Opi(-) phenotype is conditional because PA can be shuttled through a salvage pathway (Kennedy pathway) by adding choline to the growth medium. Seven new mutants present in the Opi(-) collection (fun26, kex1, nup84, tps1, mrpl38, mrpl49, and opi10/yol032w) were also suppressed by choline, suggesting that these affect PC synthesis. Regulation in response to inositol is also coordinated with the unfolded protein response (UPR). Consistent with this, several Opi(-) mutants were found to affect the UPR (yhi9, ede1, and vps74).},
	keywords = {Gene Expression Regulation, Fungal, Genes, Fungal, Genes, Reporter, Genome, Fungal, Genomics, Inositol, Lac Operon, Models, Biological, Mutation, Phenotype, Phospholipids, Protein Folding, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins},
	issn = {0016-6731},
	doi = {10.1534/genetics.106.057489},
	author = {Hancock, Leandria C and Behta, Ryan P and Lopes, John M}
}
@article {694,
	title = {Identification of a novel protein with a role in lipoarabinomannan biosynthesis in mycobacteria.},
	journal = {J Biol Chem},
	volume = {281},
	year = {2006},
	month = {2006 Apr 7},
	pages = {9011-7},
	abstract = {All species of Mycobacteria synthesize distinctive cell walls that are rich in phosphatidylinositol mannosides (PIMs), lipomannan (LM), and lipoarabinomannan (LAM). PIM glycolipids, having 2-4 mannose residues, can either be channeled into polar PIM species (with 6 Man residues) or hypermannosylated to form LM and LAM. In this study, we have identified a Mycobacterium smegmatis gene, termed lpqW, that is required for the conversion of PIMs to LAM and is highly conserved in all mycobacteria. A transposon mutant, Myco481, containing an insertion near the 3{\textquoteright} end of lpqW exhibited altered colony morphology on complex agar medium. This mutant was unstable and was consistently overgrown by a second mutant, represented by Myco481.1, that had normal growth and colony characteristics. Biochemical analysis and metabolic labeling studies showed that Myco481 synthesized the complete spectrum of apolar and polar PIMs but was unable to make LAM. LAM biosynthesis was restored to near wild type levels in Myco481.1. However, this mutant was unable to synthesize the major polar PIM (AcPIM6) and accumulated a smaller intermediate, AcPIM4. Targeted disruption of the lpqW gene and complementation of the initial Myco481 mutant with the wild type gene confirmed that the phenotype of this mutant was due to loss of LpqW. These studies suggest that LpqW has a role in regulating the flux of early PIM intermediates into polar PIM or LAM biosynthesis. They also suggest that AcPIM4 is the likely branch point intermediate in polar PIM and LAM biosynthesis.},
	keywords = {Cell Membrane, Gene Expression Regulation, Bacterial, Genes, Bacterial, Lipopolysaccharides, Mutation, Mycobacterium smegmatis, Phenotype, Phosphatidylinositols, Virulence},
	issn = {0021-9258},
	doi = {10.1074/jbc.M511709200},
	author = {Kovacevic, Svetozar and Anderson, Dianne and Morita, Yasu S and Patterson, John and Haites, Ruth and McMillan, Benjamin N I and Coppel, Ross and McConville, Malcolm J and Billman-Jacobe, Helen}
}
@article {819,
	title = {A novel dnaC mutation that suppresses priB rep mutant phenotypes in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {60},
	year = {2006},
	month = {2006 May},
	pages = {973-83},
	abstract = {The loading of a replisome in prokaryotic and eukaryotic cells at an origin of DNA replication and during replication restart is a highly ordered and regulated process. During replication restart in Escherichia coli, the PriA, PriB, PriC, DnaT and Rep proteins form multiple pathways that bind to repaired replication forks. These complexes are then recognized by DnaC as sites to load DnaB, the replicative helicase. Several dnaC mutations have been isolated that suppress phenotypes of some replication restart mutants. A new dnaC mutation (dnaC824) is reported here that efficiently suppresses priB rep mutant phenotypes. Furthermore, it is shown that dnaC824 will suppress phenotypes of priB priA300, rep priA300 and priB priC strains. Unlike other dnaC suppressors, it can only weakly suppress the absence of priA. Others have reported a different type of dnaC mutation, dnaC1331, is able to mimic priB mutant phenotypes. This is supported herein by showing that like dnaC1331, a priB mutation is synthetically lethal with a dam mutation and this can be rescued by a mutH mutation. Furthermore, priB dam lethality can also be suppressed by dnaC824. Like a priB mutation, a dnaC1331 mutation causes a priA2::kan-like phenotype when combined with priA300. Lastly, we show that dnaC824 is dominant to wild type and that dnaC1331 is recessive to wild type. Several models are discussed for the action of these mutant dnaC proteins in replication restart.},
	keywords = {DNA Replication, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Dominant, Genes, Lethal, Genes, Recessive, Mutant Proteins, Mutation, Phenotype, Suppression, Genetic},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2006.05147.x},
	author = {Boonsombat, Ruethairat and Yeh, Su-Ping and Milne, Amy and Sandler, Steven J}
}
@article {39,
	title = {Phosphatidylinositol biosynthesis: biochemistry and regulation.},
	journal = {Biochim Biophys Acta},
	volume = {1735},
	year = {2005},
	month = {2005 Jul 15},
	pages = {89-100},
	abstract = {Phosphatidylinositol (PI) is a ubiquitous membrane lipid in eukaryotes. It is becoming increasingly obvious that PI and its metabolites play a myriad of very diverse roles in eukaryotic cells. The Saccharomyces cerevisiae PIS1 gene is essential and encodes PI synthase, which is required for the synthesis of PI. Recently, PIS1 expression was found to be regulated in response to carbon source and oxygen availability. It is particularly significant that the promoter elements required for these responses are conserved evolutionarily throughout the Saccharomyces genus. In addition, several genome-wide strategies coupled with more traditional screens suggest that several other factors regulate PIS1 expression. The impact of regulating PIS1 expression on PI synthesis will be discussed along with the possible role(s) that this may have on diseases such as cancer.},
	keywords = {Eukaryotic Cells, Gene Expression Regulation, Fungal, Mutation, Phenotype, Phosphatidylinositols, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transferases (Other Substituted Phosphate Groups)},
	issn = {0006-3002},
	doi = {10.1016/j.bbalip.2005.05.006},
	author = {Gardocki, Mary E and Jani, Niketa and Lopes, John M}
}
@article {821,
	title = {Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12.},
	journal = {Genetics},
	volume = {169},
	year = {2005},
	month = {2005 Apr},
	pages = {1799-806},
	abstract = {Constitutive stable DNA replication (cSDR) is a mechanism for replisome loading in Escherichia coli K-12. This occurs in a dnaA-independent fashion in an rnhA mutant. cSDR is dependent on recA, priA, and transcription. In this report, it is shown that dnaA rnhA mutants using cSDR for initiation of their DNA replication additionally require priB, but not priC, for viability. Two subtle priA missense mutations either eliminated the ability to grow using cSDR (priA301 C479Y) or resulted in very small colonies (priA300 K230R). DnaC809, a priA suppressor, failed to allow priA or priB mutants to grow using cSDR to initiate DNA replication. Furthermore, unlike dnaC(+) strains, dnaC809 strains require priC for cSDR. DnaC809,820, a priC-independent suppressor of priA2::kan phenotypes, allowed priA and priC (but not priB) mutants to grow using cSDR to initiate DNA replication. It is also shown that rep and rnhA mutations are synthetically lethal. DnaC809 and dnaC809,820 mutations suppress this lethality. Rep is further shown to be required for cSDR in a dnaC809 strain. A model whereby these different sets of replication restart proteins interact preferentially with substrates associated with either RecA or SSB during replication restart and cSDR, respectively, is proposed.},
	keywords = {Bacterial Proteins, DNA, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genome, Bacterial, Macromolecular Substances, Models, Genetic, Mutation, Mutation, Missense, Phenotype, Rec A Recombinases, RNA, SOS Response (Genetics)},
	issn = {0016-6731},
	doi = {10.1534/genetics.104.036962},
	author = {Sandler, Steven J}
}
@article {555,
	title = {Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {186},
	year = {2004},
	month = {2004 May},
	pages = {3022-8},
	abstract = {Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement. Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors. Hya, in contrast, was not. These findings suggest that Hyb is an essential respiratory hydrogenase in G. sulfurreducens.},
	keywords = {Anthraquinones, Ferric Compounds, Fumarates, Geobacter, Hydrogen, Operon, Oxidation-Reduction, Oxidoreductases, Phenotype},
	issn = {0021-9193},
	author = {Coppi, Maddalena V and O{\textquoteright}Neil, Regina A and Lovley, Derek R}
}
@article {41,
	title = {Identification of novel dominant INO2c mutants with an Opi- phenotype.},
	journal = {Mol Microbiol},
	volume = {52},
	year = {2004},
	month = {2004 Jun},
	pages = {1271-80},
	abstract = {The INO2 gene of Saccharomyces cerevisiae is required for derepression of the phospholipid biosynthetic genes in response to inositol depletion. Conversely, the OPI1 gene is required for repression in response to inositol supplementation. Results of an in vitro assay have led to a model in which Opi1p interacts with Ino2p. However, there is no in vivo evidence to support this model. Additionally, most of the previously isolated ino2 mutants offer little insight into this model. Here, we report the isolation of a new class of dominant mutations in the INO2 gene, which yield constitutive expression of a target gene (i.e. an Opi(-) mutant phenotype). Two mutations reside in a region of the Ino2p required for interaction with Opi1p in vitro. Three other mutations are at the amino-terminus in a transcriptional activation domain.},
	keywords = {Basic Helix-Loop-Helix Transcription Factors, Gene Expression Regulation, Fungal, Inositol, Mutation, Phenotype, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2004.04069.x},
	author = {Gardenour, Kyle R and Levy, Jamie and Lopes, John M}
}
@article {774,
	title = {Quorum sensing in Staphylococci is regulated via phosphorylation of three conserved histidine residues.},
	journal = {J Biol Chem},
	volume = {279},
	year = {2004},
	month = {2004 Apr 9},
	pages = {14665-72},
	abstract = {Staphylococcus aureus cause infections by producing toxins, a process regulated by cell-cell communication (quorum sensing) through the histidine-phosphorylation of the target of RNAIII-activating protein (TRAP). We show here that TRAP is highly conserved in staphylococci and contains three completely conserved histidine residues (His-66, His-79, His-154) that are phosphorylated and essential for its activity. This was tested by constructing a TRAP(-) strain with each of the conserved histidine residues changed to alanine by site-directed mutagenesis. All mutants were tested for pathogenesis in vitro (expression of RNAIII and hemolytic activity) and in vivo (murine cellulitis model). Results show that RNAIII is not expressed in the TRAP(-) strain, that it is non hemolytic, and that it does not cause disease in vivo. These pathogenic phenotypes could be rescued in the strain containing the recovered traP, confirming the importance of TRAP in S. aureus pathogenesis. The phosphorylation of TRAP mutated in any of the conserved histidine residues was significantly reduced, and mutants defective in any one of these residues were non-pathogenic in vitro or in vivo, whereas those mutated in a non-conserved histidine residue (His-124) were as pathogenic as the wild type. These results confirm the importance of the three conserved histidine residues in TRAP activity. The phosphorylation pattern, structure, and gene organization of TRAP deviates from signaling molecules known to date, suggesting that TRAP belongs to a novel class of signal transducers.},
	keywords = {Amino Acid Sequence, Animals, Blotting, Northern, Cell Communication, DNA, Electrophoresis, Polyacrylamide Gel, Escherichia coli, Histidine, Mice, Molecular Sequence Data, Mutagenesis, Mutagenesis, Site-Directed, Mutation, Phenotype, Phosphorylation, Phylogeny, Plasmids, Protein Structure, Tertiary, RNA, Antisense, RNA, Bacterial, Sequence Homology, Amino Acid, Signal Transduction, Staphylococcus aureus, Time Factors},
	issn = {0021-9258},
	doi = {10.1074/jbc.M311106200},
	author = {Gov, Yael and Borovok, Ilya and Korem, Moshe and Singh, Vineet K and Jayaswal, Radheshyam K and Wilkinson, Brian J and Rich, Stephen M and Balaban, Naomi}
}
@article {43,
	title = {Opi1p, Ume6p and Sin3p control expression from the promoter of the INO2 regulatory gene via a novel regulatory cascade.},
	journal = {Mol Microbiol},
	volume = {48},
	year = {2003},
	month = {2003 May},
	pages = {823-32},
	abstract = {The INO2 gene of Saccharomyces cerevisiae is required for expression of most of the phospholipid biosynthetic genes. INO2 expression is regulated by a complex cascade that includes autoregulation, Opi1p-mediated repression and Ume6p-mediated activation. To screen for mutants with altered INO2 expression directly, we constructed an INO2-HIS3 reporter that provides a plate assay for INO2 promoter activity. This reporter was used to isolate mutants (dim1) that fail to repress expression of the INO2 gene in an otherwise wild-type strain. The dim1 mutants contain mutations in the OPI1 gene. To define further the mechanism for Ume6p regulation of INO2 expression, we isolated suppressors (rum1, 2, 3) of the ume6Delta mutation that overexpress the INO2-HIS3 gene. Two of the rum mutant groups contain mutations in the OPI1 and SIN3 genes showing that opi1 and sin3 mutations are epistatic to the ume6Delta mutation. These results are surprising given that Ume6p, Sin3p and Rpd3p are known to form a complex that represses the expression of a diverse set of yeast genes. This prompted us to examine the effect of sin3Delta and rpd3Delta mutants on INO2-cat expression. Surprisingly, the sin3Delta allele overexpressed INO2-cat, whereas the rpd3Delta mutant had no effect. We also show that the UME6 gene does not affect the expression of an OPI1-cat reporter. This suggests that Ume6p does not regulate INO2 expression indirectly by regulating OPI1 expression.},
	keywords = {Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Fungal Proteins, Gene Expression Regulation, Fungal, Genes, Regulator, Genes, Reporter, Genetic Complementation Test, Histone Deacetylases, Methyltransferases, Phenotype, Phospholipids, Promoter Regions, Genetic, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors},
	issn = {0950-382X},
	author = {Kaadige, Mohan R and Lopes, John M}
}
@article {399,
	title = {A comprehensive alanine scanning mutagenesis of the Escherichia coli transcriptional activator SoxS: identifying amino acids important for DNA binding and transcription activation.},
	journal = {J Mol Biol},
	volume = {322},
	year = {2002},
	month = {2002 Sep 13},
	pages = {237-57},
	abstract = {SoxS is the direct transcriptional activator of the superoxide regulon. SoxS recognizes a highly degenerate "soxbox" DNA sequence, and activates transcription from class I and class II promoters. SoxS is the smallest member of the AraC/XylS family of transcription regulators whose hallmark is dual helix-turn-helix (HTH) DNA-binding motifs. Evidence suggests that the N-terminal HTH motif of SoxS interacts with a highly conserved region of the soxbox termed recognition element 1 (RE1), while the C-terminal HTH motif interacts with the less conserved recognition element 2 (RE2). In the work described here, we prepared a complete library of 101 SoxS mutants containing single alanine substitutions of SoxS, and we characterized the mutant proteins in vivo and in vitro. With SoxS being closely related to MarA, we analyzed the effects of the SoxS mutations in the context of the MarA-mar crystal structure and with respect to the NMR study of MarA-DNA complexes in solution. From the properties of the alanine substitutions, we conclude the following. (1) Surface-exposed residues of helix 3 and helix 6, the recognition helices of the dual HTH motifs, are important to DNA binding and transcription activation; however, substitutions of residues predicted from the MarA-mar crystal structure to make contact with the sugar-phosphate backbone are more detrimental to DNA binding than mutations predicted to make base-specific contacts. (2) Substitution of several residues within the recognition helix predicted to make base-specific contacts with RE2 have relatively little effect on DNA-binding, suggesting the possibility of alternative protein-DNA interactions than those inferred from the MarA-mar crystal structure. (3) DNA binding and transcription activation were reduced by substitution of conserved amino acid residues comprising the hydrophobic core, presumably because they disrupt the structural integrity of SoxS. (4) Mutant K30A appears to be a positive control mutant defective in a protein-protein interaction with RNA polymerase that is required for transcription activation at all SoxS-dependent promoters because it binds and bends DNA normally but fails to activate transcription from both classes of promoters. Alanine substitutions of surface-exposed residues H3, K5, D9, S31, and V45 confer a similar phenotype. Since these residues are near K30 on the surface of the protein, the surface formed by the six residues may be used to make protein-protein interactions with RNA polymerase that are required for transcription activation at both class I and class II SoxS-dependent promoters. (5) Mutants F74A, D75A, M78A, D79A and Q85A appear to define a surface required for protein-protein interaction with RNA polymerase specifically at class II promoters because these positive control mutants bind and bend DNA normally but are defective in activation of class II promoters but not class I promoters. These SoxS mutants that bind and bend DNA normally but are defective in transcription activation represent the first positive control mutants with putative defects in protein-protein interactions with RNA polymerase among the SoxS/MarA/Rob subset of the AraC/XylS family of transcription regulators.},
	keywords = {Alanine, Amino Acid Substitution, Base Sequence, Binding Sites, DNA, DNA-Binding Proteins, Electrophoretic Mobility Shift Assay, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Lethal, Hydrophobic and Hydrophilic Interactions, Lac Operon, Models, Molecular, Mutagenesis, Nucleic Acid Conformation, Phenotype, Phosphates, Promoter Regions, Genetic, Protein Binding, Protein Structure, Tertiary, Structure-Activity Relationship, Trans-Activators, Transcriptional Activation},
	issn = {0022-2836},
	author = {Griffith, Kevin L and Wolf, Richard E}
}
@article {574,
	title = {Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds.},
	journal = {Int J Syst Evol Microbiol},
	volume = {52},
	year = {2002},
	month = {2002 Nov},
	pages = {1929-35},
	abstract = {Strain 853-15A(T) was enriched and isolated from uranium-contaminated aquifer sediment by its ability to grow under anaerobic conditions via the oxidation of lactate coupled to the reduction of anthraquinone-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Lactate was oxidized incompletely to acetate and carbon dioxide according to the reaction CH3CHOHCOO(-)+ 2AQDS+H2O --> CH3COO(-)+ 2AHQDS+CO2. Additional electron donors utilized included formate, ethanol, butanol, butyrate, malate and pyruvate. Lactate also supported growth with Fe(III) citrate, Mn(IV) oxide, humic substances, elemental sulfur, 3-chloro-4-hydroxyphenylacetate, trichloroethylene or tetrachloroethylene serving as the electron acceptor. Growth was not observed with sulfate, sulfite, nitrate or fumarate as the terminal electron acceptor. The temperature optimum for growth was 30 degrees C, but growth was also observed at 20 and 37 degrees C. The pH optimum was approximately 7.0. The 16S rDNA sequence of strain 853-15A(T) suggested that it was most closely related to Desulfitobacterium dehalogenans and closely related to Desulfitobacterium chlororespirans and Desulfitobacterium frappieri. The phylogenetic and physiological properties exhibited by strain 853-15A(T) (= ATCC BAA-636(T)) place it within the genus Desulfitobacterium as the type strain of a novel species, Desulfitobacterium metallireducens sp. nov.},
	keywords = {Anaerobiosis, DNA, Bacterial, DNA, Ribosomal, Ecosystem, Electron Transport, Geologic Sediments, Humic Substances, Metals, Microscopy, Electron, Molecular Sequence Data, Oxidation-Reduction, Peptococcaceae, Phenotype, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Species Specificity},
	issn = {1466-5026},
	author = {Finneran, Kevin T and Forbush, Heather M and VanPraagh, Catherine V Gaw and Lovley, Derek R}
}
@article {825,
	title = {PriA mutations that affect PriA-PriC function during replication restart.},
	journal = {Mol Microbiol},
	volume = {41},
	year = {2001},
	month = {2001 Aug},
	pages = {697-704},
	abstract = {In Escherichia coli, repair and restart of collapsed replication forks is thought to be essential for cell growth. The replication restart proteins, PriA, PriB, PriC, DnaB, DnaC, DnaG, DnaT and Rep, form redundant pathways that recognize repaired replication forks and restart them. Recognition, modulation of specific DNA structures and loading of the replicative helicase by the replication restart proteins, is likely to be important for replication restart. It has been hypothesized that PriB and PriC function with PriA in genetically separate and redundant PriA-PriB and PriA-PriC pathways. In this study, the del(priB)302 or priC303:kan mutations were used to isolate the PriA-PriB and PriA-PriC pathways genetically so that the effects of three priA missense mutations, priA300 (K230R), priA301 (C479Y) and priA306 (L557P), on these pathways could be assessed. In a wild-type background, the three priA mutations had little, if any, effect on the phenotypes of UV resistance, basal levels of SOS expression and cell viability. In the priB mutant, priA300 and priA301 caused dramatic negative changes in the three phenotypes listed above (and others), whereas the third priA mutant allele, priA306, showed very little negative effect. In the priC mutant, all three priA mutations behaved similarly, producing little, if any, changes in phenotypes. We conclude that priA300 and priA301 mostly affect the PriA-PriC pathway and do so more than priA306. We suggest that PriA{\textquoteright}s helicase activity is important for the PriA-PriC pathway of replication restart.},
	keywords = {Bacterial Proteins, Bacteriophage mu, Cell Division, DNA Replication, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Lethal, Genotype, Models, Biological, Mutation, Missense, Phenotype, Replication Protein A, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0950-382X},
	author = {Sandler, S J and McCool, J D and Do, T T and Johansen, R U}
}
@article {830,
	title = {dnaC mutations suppress defects in DNA replication- and recombination-associated functions in priB and priC double mutants in Escherichia coli K-12.},
	journal = {Mol Microbiol},
	volume = {34},
	year = {1999},
	month = {1999 Oct},
	pages = {91-101},
	abstract = {PriA, PriB and PriC were originally discovered as proteins essential for the PhiX174 in vitro DNA replication system. Recent studies have shown that PriA mutants are poorly viable, have high basal levels of SOS expression (SOSH), are recombination deficient (Rec-), sensitive to UV irradiation (UVS) and sensitive to rich media. These data suggest that priA{\textquoteright}s role may be more complex than previously thought and may involve both DNA replication and homologous recombination. Based on the PhiX174 system, mutations in priB and priC should cause phenotypes like those seen in priA2:kan mutants. To test this, mutations in priB and priC were constructed. We found that, contrary to the PhiX174 model, del(priB)302 and priC303:kan mutants have almost wild-type phenotypes. Most unexpectedly, we then found that the priBC double mutant had very poor viability and/or a slow growth rate (even less than a priA2:kan mutant). This suggests that priB and priC have a redundant and important role in Escherichia coli. The priA2:kan suppressor, dnaC809, partially suppressed the poor viability/slow growth phenotype of the priBC double mutant. The resulting triple mutant (priBC dnaC809 ) had small colony size, recombination deficiency and levels of SOS expression similar to a priA2:kan mutant. The priBC dnaC809 mutant, however, was moderately UVR and had good viability, unlike a priA2:kan mutant. Additional mutations in the triple mutant were selected to suppress the slow growth phenotype. One suppressor restored all phenotypes tested to nearly wild-type levels. This mutation was identified as dnaC820 (K178N) [mapping just downstream of dnaC809 (E176G)]. Experiments suggest that dnaC820 makes dnaC809 suppression of priA and or priBC mutants priB and or priC independent. A model is proposed for the roles of these proteins in terms of restarting collapsed replication forks from recombinational intermediates.},
	keywords = {Bacterial Proteins, Bacteriophage mu, Cell Division, DNA Replication, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Mutation, Phenotype, Recombination, Genetic, Replication Protein A, SOS Response (Genetics), Substrate Specificity, Suppression, Genetic},
	issn = {0950-382X},
	author = {Sandler, S J and Marians, K J and Zavitz, K H and Coutu, J and Parent, M A and Clark, A J}
}
@article {836,
	title = {Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC.},
	journal = {Genetics},
	volume = {143},
	year = {1996},
	month = {1996 May},
	pages = {5-13},
	abstract = {First identified as an essential component of the phi X174 in vitro DNA replication system, PriA has ATPase, helicase, translocase, and primosome-assembly activities. priA1::kan strains of Escherichia coli are sensitive to UV irradiation, deficient in homologous recombination following transduction, and filamentous. priA2::kan strains have eightfold higher levels of uninduced SOS expression than wild type. We show that (1) priA1::kan strains have eightfold higher levels of uninduced SOS expression, (2) priA2::kan strains are UVS and Rec-, (3) lexA3 suppresses the high basal levels of SOS expression of a priA2::kan strain, and (4) plasmid-encoded priA300 (K230R), a mutant allele retaining only the primosome-assembly activity of priA+, restores both UVR and Rec+ phenotypes to a priA2::kan strain. Finally, we have isolated 17 independent UVR Rec+ revertants of priA2::kan strains that carry extragenic suppressors. All 17 map in the C-terminal half of the dnaC gene. DnaC loads the DnaB helicase onto DNA as a prelude for primosome assembly and DNA replication. We conclude that priA{\textquoteright}s primosome-assembly activity is essential for DNA repair and recombination and that the dnaC suppressor mutations allow these processes to occur in the absence of priA.},
	keywords = {Bacterial Proteins, Bacteriophage phi X 174, beta-Galactosidase, Chromosomes, Bacterial, DNA Helicases, DNA Replication, DNA-Binding Proteins, Dose-Response Relationship, Radiation, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Genetic Markers, Mutagenesis, Phenotype, Recombination, Genetic, Replication Protein A, Repressor Proteins, Serine Endopeptidases, Suppression, Genetic, Transduction, Genetic, Ultraviolet Rays},
	issn = {0016-6731},
	author = {Sandler, S J and Samra, H S and Clark, A J}
}
@article {841,
	title = {RecOR suppression of recF mutant phenotypes in Escherichia coli K-12.},
	journal = {J Bacteriol},
	volume = {176},
	year = {1994},
	month = {1994 Jun},
	pages = {3661-72},
	abstract = {The recF, recO, and recR genes form the recFOR epistasis group for DNA repair. recF mutants are sensitive to UV irradiation and fail to properly induce the SOS response. Using plasmid derivatives that overexpress combinations of the recO+ and recR+ genes, we tested the hypothesis that high-level expression of recO+ and recR+ (recOR) in vivo will indirectly suppress the recF mutant phenotypes mentioned above. We found that overexpression of just recR+ from the plasmid will partially suppress both phenotypes. Expression of the chromosomal recO+ gene is essential for the recR+ suppression. Hence we call this RecOR suppression of recF mutant phenotypes. RecOR suppression of SOS induction is more efficient with recO+ expression from a plasmid than with recO+ expression from the chromosome. This is not true for RecOR suppression of UV sensitivity (the two are equal). Comparison of RecOR suppression with the suppression caused by recA801 and recA803 shows that RecOR suppression of UV sensitivity is more effective than recA803 suppression and that RecOR suppression of UV sensitivity, like recA801 suppression, requires recJ+. We present a model that explains the data and proposes a function for the recFOR epistasis group in the induction of the SOS response and recombinational DNA repair.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Damage, DNA Repair, DNA-Binding Proteins, Epistasis, Genetic, Escherichia coli, Escherichia coli Proteins, Models, Genetic, Molecular Sequence Data, Phenotype, Plasmids, SOS Response (Genetics), Suppression, Genetic, Ultraviolet Rays},
	issn = {0021-9193},
	author = {Sandler, S J and Clark, A J}
}
@article {843,
	title = {Use of high and low level overexpression plasmids to test mutant alleles of the recF gene of Escherichia coli K-12 for partial activity.},
	journal = {Genetics},
	volume = {135},
	year = {1993},
	month = {1993 Nov},
	pages = {643-54},
	abstract = {We showed that sufficient overexpression of the wild-type recF gene interfered with three normal cell functions: (1) UV induction of transcription from the LexA-protein-repressed sulA promoter, (2) UV resistance and (3) cell viability at 42 degrees. To show this, we altered a low-level overexpressing recF+ plasmid with a set of structurally neutral mutations that increased the rate of expression of recF. The resulting high-level overexpressing plasmid interfered with UV induction of the sulA promoter, as did the low-level overexpressing plasmid. It also reduced UV resistance more than its low level progenitor and decreased viability at 42 degrees, an effect not seen with the low-level plasmid. We used the high-level plasmid to test four recF structural mutations for residual activity. The structural alleles consisted of an insertion mutation, two single amino acid substitution mutations and a double amino acid substitution mutation. On the Escherichia coli chromosome the three substitution mutations acted similarly to a recF deletion in reducing UV resistance in a recB21 recC22 sbcB15 sbcC201 genetic background. By this test, therefore, all three appeared to be null alleles. Measurements of conjugational recombination revealed, however, that the three substitution mutations may have residual activity. On the high-level overexpressing plasmid all three substitution mutations definitely showed partial activity. By contrast, the insertion mutation on the high-level overexpressing plasmid showed no partial activity and can be considered a true null mutation. One of the substitutions, recF143, showed a property attributable to a leaky mutation. Another substitution, recF4101, may block selectively two of the three interference phenotypes, thus allowing us to infer a mechanism for them.},
	keywords = {Alleles, Bacterial Proteins, Base Sequence, Chromosomes, Bacterial, DNA Repair, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression, Genes, Bacterial, Molecular Sequence Data, Mutagenesis, Site-Directed, Mutation, Phenotype, Plasmids, Radiation Tolerance, Recombination, Genetic, Ultraviolet Rays},
	issn = {0016-6731},
	author = {Sandler, S J and Clark, A J}
}
