@article {1458,
	title = {Transcription regulation of a yeast gene from a downstream location.},
	journal = {J Mol Biol},
	volume = {425},
	year = {2013},
	month = {2013 Feb 8},
	pages = {457-65},
	abstract = {<p>Mechanisms for coregulation of transcription of tandem genes in yeast remain largely speculative. This study focused on inositol-mediated regulation of the tandem gene pair SNA3-INO1. While the pattern of regulation of these two genes was similar, results showed that intermediate levels of inositol repressed INO1 and induced SNA3. Results also showed that inositol-mediated regulation of the SNA3 gene was not a function of its promoter but occurred from factors within the SNA3-INO1 intergenic region. The basic helix-loop-helix proteins, Ino2p and Ino4p, mediated this regulation through the upstream activation sequence (UAS)(INO) (E-box) sequences in the intergenic region. These results provide a model for studying coregulation of yeast tandem genes. This is especially significant given that many tandem gene pairs in yeast are coregulated even though context-specific UAS sequences are known only for one gene in the pair.</p>
},
	keywords = {Gene Expression Regulation, Fungal, Inositol, Membrane Proteins, Myo-Inositol-1-Phosphate Synthase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2012.11.018},
	author = {Shetty, Ameet and Swaminathan, Aishwarya and Lopes, John M}
}
@article {690,
	title = {Direct recognition of the mycobacterial glycolipid, trehalose dimycolate, by C-type lectin Mincle.},
	journal = {J Exp Med},
	volume = {206},
	year = {2009},
	month = {2009 Dec 21},
	pages = {2879-88},
	abstract = {Tuberculosis remains a fatal disease caused by Mycobacterium tuberculosis, which contains various unique components that affect the host immune system. Trehalose-6,6{\textquoteright}-dimycolate (TDM; also called cord factor) is a mycobacterial cell wall glycolipid that is the most studied immunostimulatory component of M. tuberculosis. Despite five decades of research on TDM, its host receptor has not been clearly identified. Here, we demonstrate that macrophage inducible C-type lectin (Mincle) is an essential receptor for TDM. Heat-killed mycobacteria activated Mincle-expressing cells, but the activity was lost upon delipidation of the bacteria; analysis of the lipid extracts identified TDM as a Mincle ligand. TDM activated macrophages to produce inflammatory cytokines and nitric oxide, which are completely suppressed in Mincle-deficient macrophages. In vivo TDM administration induced a robust elevation of inflammatory cytokines in sera and characteristic lung inflammation, such as granuloma formation. However, no TDM-induced lung granuloma was formed in Mincle-deficient mice. Whole mycobacteria were able to activate macrophages even in MyD88-deficient background, but the activation was significantly diminished in Mincle/MyD88 double-deficient macrophages. These results demonstrate that Mincle is an essential receptor for the mycobacterial glycolipid, TDM.},
	keywords = {Animals, Cord Factors, Granuloma, Lectins, C-Type, Ligands, Lung Diseases, Macrophage Activation, Membrane Proteins, Mice, Mice, Inbred C57BL, Myeloid Differentiation Factor 88, Receptors, IgG},
	issn = {1540-9538},
	doi = {10.1084/jem.20091750},
	author = {Ishikawa, Eri and Ishikawa, Tetsuaki and Morita, Yasu S and Toyonaga, Kenji and Yamada, Hisakata and Takeuchi, Osamu and Kinoshita, Taroh and Akira, Shizuo and Yoshikai, Yasunobu and Yamasaki, Sho}
}
@article {470,
	title = {Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.},
	journal = {BMC Genomics},
	volume = {9},
	year = {2008},
	month = {2008},
	pages = {471},
	abstract = {BACKGROUND: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells.

RESULTS: The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors sigma28 and sigma54 play a role in regulating the Geobacter chemotaxis gene expression.

CONCLUSION: The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Chemotaxis, Escherichia coli, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Geobacter, Membrane Proteins, Molecular Sequence Data, Multigene Family, Promoter Regions, Genetic, Sequence Alignment, Sequence Homology, Amino Acid},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-9-471},
	author = {Tran, Hoa T and Krushkal, Julia and Antommattei, Frances M and Lovley, Derek R and Weis, Robert M}
}
@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}
}
@article {1219,
	title = {Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus.},
	journal = {J Bacteriol},
	volume = {183},
	year = {2001},
	month = {2001 Jan},
	pages = {716-24},
	abstract = {<p>The hyperthermophilic archaeon Pyrococcus furiosus grows optimally at 100 degrees C by the fermentation of peptides and carbohydrates. Growth of the organism was examined in media containing either maltose, peptides (hydrolyzed casein), or both as the carbon source(s), each with and without elemental sulfur (S(0)). Growth rates were highest on media containing peptides and S(0), with or without maltose. Growth did not occur on the peptide medium without S(0). S(0) had no effect on growth rates in the maltose medium in the absence of peptides. Phenylacetate production rates (from phenylalanine fermentation) from cells grown in the peptide medium containing S(0) with or without maltose were the same, suggesting that S(0) is required for peptide utilization. The activities of 14 of 21 enzymes involved in or related to the fermentation pathways of P. furiosus were shown to be regulated under the five different growth conditions studied. The presence of S(0) in the growth media resulted in decreases in specific activities of two cytoplasmic hydrogenases (I and II) and of a membrane-bound hydrogenase, each by an order of magnitude. The primary S(0)-reducing enzyme in this organism and the mechanism of the S(0) dependence of peptide metabolism are not known. This study provides the first evidence for a highly regulated fermentation-based metabolism in P. furiosus and a significant regulatory role for elemental sulfur or its metabolites.</p>},
	keywords = {Culture Media, Cytoplasm, Gene Expression Regulation, Archaeal, Gene Expression Regulation, Enzymologic, Glycolysis, Hydrogenase, Membrane Proteins, Oxidation-Reduction, Peptides, Pyrococcus furiosus, Sulfur},
	issn = {0021-9193},
	doi = {10.1128/JB.183.2.716-724.2001},
	author = {Adams, M W and Holden, J F and Menon, A L and Schut, G J and Grunden, A M and Hou, C and Hutchins, A M and Jenney, F E and Kim, C and Ma, K and Pan, G and Roy, R and Sapra, R and Story, S V and Verhagen, M F}
}
@article {710,
	title = {Extracellular simian virus 40 transmits a signal that promotes virus enclosure within caveolae.},
	journal = {Exp Cell Res},
	volume = {246},
	year = {1999},
	month = {1999 Jan 10},
	pages = {83-90},
	abstract = {It was reported earlier that entry of simian virus 40 (SV40) into cells is promoted by a signal transmitted by the virus from the cell surface and that SV40 enters cells through caveolae. It is shown here that bound SV40 begins to partition into a caveolae-enriched Triton X-100-insoluble membrane fraction at 30 min postadsorption. Maximal levels of SV40 were seen in that fraction at 1 h. The sterol-binding agent nystatin, which selectively disrupts the cholesterol-enriched caveolae-containing membrane microdomain, selectively blocked the SV40-induced signal. This implies that the SV40 signal is transmitted from that membrane microdomain. The tyrosine kinase inhibitor genistein, which was earlier shown to block the SV40-induced signal and infectious entry, did not block the partitioning of SV40 into the detergent-insoluble membrane fraction. This shows that the signal is not required for the translocation of SV40 to the detergent-insoluble membrane and is consistent with the finding that the signal is likely transmitted from that membrane microdomain. However, electron microscopy of the Triton X-100-insoluble membrane fraction showed that genistein caused SV40 particles to accumulate at the annuli or mouths of the caveolae. In contrast, most SV40 particles were found enclosed within caveolae in parallel samples from untreated control cells. Together, these results imply that SV40 initially binds to flat detergent-soluble membrane. The virus then translocates to a caveolae-containing detergent-insoluble membrane microdomain. From the flat portion of that membrane microdomain the virus induces a signal which promotes its entry into caveolae.},
	keywords = {Animals, Blotting, Northern, Blotting, Western, Caveolin 1, Caveolins, Cell Line, Cell Membrane, Cercopithecus aethiops, Cholesterol, Endocytosis, Genes, myc, Genistein, Kidney, Membrane Proteins, Microscopy, Electron, Nystatin, Octoxynol, Signal Transduction, Simian virus 40, Solubility},
	issn = {0014-4827},
	doi = {10.1006/excr.1998.4301},
	author = {Chen, Y and Norkin, L C}
}
@article {709,
	title = {MHC class I molecules are enriched in caveolae but do not enter with simian virus 40.},
	journal = {J Gen Virol},
	volume = {79 ( Pt 6)},
	year = {1998},
	month = {1998 Jun},
	pages = {1469-77},
	abstract = {Simian virus 40 (SV40) binds to MHC class I molecules anywhere on the cell surface and then enters through caveolae. The fate of class I molecules after SV40 binding is not known. Sensitivity of 125I-surface-labelled class I molecules to papain cleavage was used to distinguish internalized class I molecules from class I molecules remaining at the cell surface. Whereas the caveolae-enriched membrane microdomain was found to also be enriched for class I molecules, no internalized papain-resistant 125I-surface-labelled class I molecules could be detected at any time in either control cells or in cells preadsorbed with saturating amounts of SV40. Instead, 125I-surface-labelled class I molecules, as well as preadsorbed 125I-labelled anti-class I antibodies, accumulated in the medium, coincident with the turnover of class I molecules at the cell surface. The class I heavy chains that accumulated in the medium were truncated and their release was specifically prevented by the metalloprotease inhibitor 1,10-phenanthroline. Thus, whereas class I molecules mediate SV40 binding, they do not appear to mediate SV40 entry.},
	keywords = {Animals, Caveolin 1, Caveolins, Cell Line, Cell Membrane, Cercopithecus aethiops, Histocompatibility Antigens Class I, Humans, Membrane Proteins, Simian virus 40},
	issn = {0022-1317},
	author = {Anderson, H A and Chen, Y and Norkin, L C}
}
@article {708,
	title = {Bound simian virus 40 translocates to caveolin-enriched membrane domains, and its entry is inhibited by drugs that selectively disrupt caveolae.},
	journal = {Mol Biol Cell},
	volume = {7},
	year = {1996},
	month = {1996 Nov},
	pages = {1825-34},
	abstract = {Simian virus 40 (SV40) entry leading to infection occurred only after the virus was at the cell surface for 1.5 to 2 h. SV40 infectious entry was not sensitive to cytosol acidification, a treatment that blocks endocytosis via clathrin-coated vesicles. Instead, SV40 infectious entry was blocked by treating cells with the phorbol ester PMA or nystatin, which selectively disrupts caveolae. In control experiments, transferrin internalization was sensitive to cytosol acidification but was not sensitive to PMA or nystatin. Also, absorbed transferrin entered cells within minutes. Finally, bound SV40 translocated to caveolin-enriched membrane complexes isolated by a Triton X-100 insolubility protocol. Treatment with nystatin did not impair SV40 binding but did block the partitioning of virus into the caveolin-enriched complexes.},
	keywords = {Animals, Antigens, Polyomavirus Transforming, Caveolin 1, Caveolins, Cell Line, Cell Membrane, Coated Vesicles, Endocytosis, Membrane Proteins, Nystatin, Organelles, Simian virus 40, Tetradecanoylphorbol Acetate},
	issn = {1059-1524},
	author = {Anderson, H A and Chen, Y and Norkin, L C}
}
@article {796,
	title = {Mosaic structure of plasmids from natural populations of Escherichia coli.},
	journal = {Genetics},
	volume = {143},
	year = {1996},
	month = {1996 Jul},
	pages = {1091-100},
	abstract = {The distribution of plasmids related to the fertility factor F was examined in the ECOR reference collection of Escherichia coli. Probes specific for four F-related genes were isolated and used to survey the collection by DNA hybridization. To estimate the genetic diversity of genes in F-like plasmids, DNA sequences were obtained for four plasmid genes. The phylogenetic relationships among the plasmids in the ECOR strains is very different from that of the strains themselves. This finding supports the view that plasmid transfer has been frequent within and between the major groups of ECOR. Furthermore, the sequences indicate that recombination between genes in plasmids takes place at a considerably higher frequency than that observed for chromosomal genes. The plasmid genes, and by inference the plasmids themselves, are mosaic in structure with different regions acquired from different sources. Comparison of gene sequences from a variety of naturally occurring plasmids suggested a plausible donor of some of the recombinant regions as well as implicating a chi site in the mechanism of genetic exchange. The relatively high rate of recombination in F-plasmid genes suggests that conjugational gene transfer may play a greater role in bacterial population structure than previously appreciated.},
	keywords = {Bacterial Proteins, Base Sequence, DNA Helicases, DNA, Bacterial, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Evolution, Molecular, Membrane Proteins, Molecular Sequence Data, Mosaicism, Nucleic Acid Hybridization, Phylogeny, Plasmids, Polymorphism, Genetic, Proteins, Recombination, Genetic, Repressor Proteins, RNA-Binding Proteins, Trans-Activators},
	issn = {0016-6731},
	author = {Boyd, E F and Hill, C W and Rich, S M and Hartl, D L}
}
