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2001 Faculty Publications

Balagopalan, L., C.A. Keller, and S.M. Abmayr. Loss-of-function mutations reveal that the Drosophila nautilus gene is not essential for embryonic myogenesis or viability. Dev. Biol. 231:374-382.

Wei, B.L., A.-M. Brun-Zinkernagel, J.W. Simecka, B.M. Prub, P. Babitzke, and T. Romeo. Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol. Microbiol. 40:245-256.

Babitzke, P., and P. Gollnick. Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183:5795-5802.

Yakhnin, H., J.E. Babiarz, A.V. Yakhnin, and P. Babitzke. Expression of the Bacillus subtilis trpEDCFBA operon is regulated by translational coupling and Rho termination factor. J. Bacteriol. 183:5918-5926.

Gudapaty, S., K. Suzuki, X. Wang, P. Babitzke, and T. Romeo. Regulatory interactions of Csr components: The RNA binding protein CsrA activates csrB transcription in Escherichia coli. J. Bacteriol. 183:6017-6027.

Gollnick, P., P. Babitzke, E. Merino, and C. Yanofsky. Aromatic amino acid metabolism in Bacillus subtilis. In: Bacillus subtilis and Its Closet Relatives: from Genes to Cells. (A. Sonenshein, ed.), pp. 233-244, American Society for Microbiology, Washington, D.C.

Yun, D., C. Krebs, G.P. Gupta, D.F. Iwig, B.H. Huynh, and J.M. Bollinger, Jr. Facile electron transfer during formation of cluster X and kinetic competence of X for tyrosyl radical production in protien R2 of ribonucleotide reductase from mouse. Biochemistry. 41:981-990.

Baldwin, J., W.C. Voegtli, N. Khidekel, P. Moenne-Loccoz, C. Krebs, A.S. Pereira, B.A. Ley, B.H. Huynh, T.M. Loehr, P.J. Riggs-Gelasco, A.C. Rosenzweig, and J.M. Bollinger, Jr. Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase. J. Am. Chem. Soc. 123:7017-7030.

Frey, P.A., and S.J. Booker. Radical mechanisms of S-adenosylmethionine-dependent enzymes. Adv. Protein Chem. 58:1-45.

Coombs, J., and J. Brenchley. Characterization of two new glycosyl hydrolases from the lactic acid bacterium Carnobacterium piscicola strain BA. Appl. Environ. Microbiol. 67:5094-5099.

Vassilieva, E.V., M.L. Antonkine, B.L. Zybailov, F. Yang, C.U. Jakobs, J.H. Golbeck, and D.A. Bryant. Electron transfer may occur in the chlorosome envelope: The CsmI and CsmJ proteins of chlorosomes are [2Fe-2S] ferredoxins. Biochemistry. 40:464-473.

Frigaard, N.-U., and D.A. Bryant. Chromosomal gene inactivation in the green sulfur bacterium Chlorobium tepidum by natural transformation. Appl. Environ. Microbiol. 67:2538-2544.

Zhao, J., G. Shen, and D.A. Bryant. Photosystem stoichiometry and state transitions in a mutant of the cyanobacterium Synechococcus sp. PCC 7002 lacking phycocyanin. Biochim. Biophys. Acta. 1505:248-257.

Bertini, I., D.A. Bryant, S. Ciurli, A. Dikiy, C.O. Fernández, C. Luchinat, N. Safarov, A.J. Vila, and J. Zhao. Backbone dynamics of plastocyanin in both oxidation states: Solution structure of the reduced form and comparison with the oxidized state. J. Biol. Chem. 276:47217-47226.

Sakuragi, Y., B. Zybailov, A.D. Jones, P.R. Chitnis, R. Bittl, S. Zech, D. Stehlik, J.H. Golbeck, and D.A. Bryant. Insertional inactivation of the menG Gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Isynechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1, 4-naphthoquinone into the A₁ site and alteration of the equilibrium constant between A₁ and F_x in Photosystem I. Biochemistry. 41:394-405.

Sakamoto, T., and D.A. Bryant. Requirement of nickel as an essential micronutrient for the utilization of urea in the marine cyanobacterium Synechococcus sp. PCC 7002. Microbes Environ. 16:177-184.

Cameron, C.E., and C. Castro. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA ploymerase. Curr. Opin. Infect. Dis. 14:757-764.

Maag, D., C. Castro, Z. Hong, and C.E. Cameron. Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin. J. Biol. Chem. 276:46094-46098.

Hong, Z., C.E. Cameron, M.P. Walker, C. Castro, N. Yao, J.Y.N. Lau, and W. Zhong. A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology. 285:6-11.

Crotty, S., C.E. Cameron, and R. Andino. RNA virus error catastrophe: Direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. USA 98:6895-6900.

Wei, L., J.S. Huhn, A. Mory, H.B. Pathak, S.V. Sosnovtsev, K.Y. Green, and C.E. Cameron. Proteinase-polymerase precursor as the active form of feline calicivirus RNA-dependent RNA polymerase. J. Virol. 75:1211-1219.

Tackett, A.J., L. Wei, C.E. Cameron, and K.D. Raney. Unwinding of nucleic acids by HCV NS3 helicase is sensitive to the structure of the duplex. Nucleic Acids Res. 29:565-572.

Ling, A.Z., R.B. Guyer, and R.A. Deering. Dictyostelium discoideum plasmid containing an AP-endonuclease upstream sequence: bleomycin induction of a luciferase reporter. Environ. Mol. Mutagen. 38:244-247.

Buss, K.R., D.C. Cooper, C. Ingram-Smith, J.G. Ferry, D.A. Sanders, and M.S. Hasson. Urkinase: Structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J. Bacteriol. 183:680-686.

Strop, P., K.S. Smith, T.M. Iverson, J.G. Ferry, and D.C. Rees. Crystal structure of the ‘cab’ type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum. J. Biol. Chem. 276:10299-10305.

Barber, R.D., and J.G. Ferry. Archaeal proteasomes. Method. Enzymol. 330:413-424.

Iyer, P.P., and J.G. Ferry. Role of arginines in coenzyme A binding and catalysis by the phosphotransacetylase from Methanosarcina thermophila. J. Bacteriol. 183:4244-4250.

Tu, C., B.C. Tripp, J.G. Ferry, and D.N. Silverman. Bicarbonate as proton donor in catalysis by Zn(II)- and Co(II)-containing carbonic anhydrases. J. Am. Chem. Soc. 123:5861-5866.

Ferry, J.G., and D.R. Boone. Genus I. Methanospirillum. In: Bergey’s Manual of Systematic Bacteriology, Vol. 1, 2^nd ed., (R. Castenholtz and D. R. Boone, eds.), pp. 264-267, The Williams and Wilkins Co., Baltimore.

Zhao, T., F. Cruz, and J.G. Ferry. Iron-sulfur flavoprotein (Isf) from Methanosarcina thermophila is the prototype of a widely distributed family. J. Bacteriol. 183:6225-6233.

Tripp, B.C., K.S. Smith, and J.G. Ferry. Carbonic anhydrase: new insights for an ancient enzyme. J. Biol. Chem. 276:48651-48618.

Miles, R.D., P.P. Iyer, and J.G. Ferry. Site-directed mutational analysis of active site residues in the acetate kinase from Methanosarcina thermophila. J. Biol. Chem. 276:45059-45064.

Ferry, J.G. Methanogenesis Biochemistry. Encyclopedia of Life Sciences, Nature Publishing Group, London, [www.els.net].

Barber, R.D., and J.G. Ferry. Methanogenesis Ecology. Encyclopedia of Life Sciences, Nature Publishing Group, London, [www.els.net].

Prins, C., and R.J. Frisque. JC virus T’ proteins encoded by alternatively spliced early mRNAs enhance T antigen-mediated viral DNA replication in human cells. J. Neuro Virol. 7:250-264.

Frisque, R.J. Structure and function of JC virus T’ protiens. J. Neuro Virol. 7:293-297.

Kim, H-S., J.W. Henson, and R.J. Frisque. Transcription and replication in the human polyomaviruses. In: Human Polyomaviruses, Molecular and Clinical Perspectives. (K. Khalili and G. L. Stoner, eds.), pp. 73-126, Wiley-Liss, Inc., New York, NY.

Weber, J.A., and C.V. Gay. Expression of translation initiation factor IF2 is regulated during osteoblast differentiation. J. Cell. Biochem. 81:700-714.

Stains, J.P., and C.V. Gay. Inhibition of Na⁺/Ca²⁺ exchange with KB-R7943 or bepridil diminishes mineral deposition by osteoblasts. J. Bone Miner. Res. 16:1434-1443.

Wu, C.-H., L. Madabusi, H. Nishioka, P. Emanuel, M. Sypes, I. Arkhipova, and D.S. Gilmour. Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter for Drosophila melanogaster. Mol. Cell. Biol. 21:1593-1602.

Pugh, B.F., and D.S. Gilmour. Genome-wide analysis of protein-DNA interactions in living cells. Genome Biol. 2:103.1-103.3.

Vassilieva, E.V., M.L. Antonkine, B.L. Zybailov, F. Yang, C.U. Jakobs, J.H. Golbeck, and D.A. Bryant. Electron transfer may occur in the chlorosome envelope: the CsmI and CsmJ proteins of chlorosomes are [2Fe-2S] ferredoxins. Biochemistry. 40:464-473.

Vassiliev, I.R., B. Kjaer, G.L. Schorner, H.V. Scheller, and J.H. Golbeck. Photoinduced transient absorption spectra of P840/P840⁺ and the FMO Protien in reaction centers of Chlorobium vibrioforme. Biophys. J. 81:382-393.

Johnson, T.W., B. Zybailov, A.D. Jones, R. Bittl, S. Zech, D. Stehlik, J.H. Golbeck, and P. Chitnis. Recruitment of a foreign quinone into the A₁ site of photosystem I. In vivo replacement of plastoquinone-9 by media-supplemented naphthoquinones in phylloquinone biosynthetic pathway mutants of Synechocystis sp. PCC 6803. J. Biol. Chem. 276:39512-39521.

Vassiliev, I.R., M.L. Antonkine, and J.H. Golbeck. Iron-sulfur clusters in Type I reaction centers. Biochim. Biophys. Acta 1507:139-160.

Sakuragi, Y., B. Zybailov, A.D. Jones, P.R. Chitnis, R. Bittl, S. Zech, D. Stehlik, J.H. Golbeck, and D.A. Bryant. Insertional inactivation of the menG Gene, encoding 2-phytyl-1,4-naphthoquinone methyltransferase of Isynechocystis sp. PCC 6803, results in the incorporation of 2-phytyl-1, 4-naphthoquinone into the A₁ Site and alteration of the equilibrium constant between A₁ and F_x in Photosystem I. Biochemistry. 41:394-405.

Tufarelli, C., A.-M. Frischauf, R. Hardison, J. Flint, and D.R. Higgs. Characterization of a widely expressed gene (LUC7-LIKE) defining the centromeric boundary of the human alpha-globin domain. Genomics. 71:307-314.

Flint, J., J. Peden, C.Tufarelli, A.-M. Frischauf, W. Miller, R. Hardison, and D.R. Higgs. Long-range sequence comparisons and regions of conserved synteny in vertebrates defines the alpha-globin domain. Hum. Mol. Genet. 10:371-382.

Hardison, R.C. New views of evolution and regulation of vertebrate beta-like globin gene clusters from an orphaned gene in marsupials. Proc. Natl. Acad. Sci. USA 98:1327-1329.

Elnitski, L., J. Li, C.T. Noguchi, W. Miller, and R. Hardison. A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region. J. Biol. Chem. 276:6289-6298.

Molete, J., H. Petrykowska, E. Bouhassira, Y.-Q. Feng, W. Miller, and R. Hardison. Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement. Mol. Cell. Biol. 21:2969-2980.

Hardison, R.C., D.H.K. Chui, C. Riemer, B. Giardine, H. Lehväslaiho, H. Wajcman, and W. Miller. Databases of human hemoglobin variants and other resources at the globin gene server. Hemoglobin. 25:183-193.

Chiaromonte, F., S. Yang, L. Elnitski, W. Miller, and R.C. Hardison. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci. USA 98:14503-14508.

Wang, X., A.L. Hughes, T. Tsukamoto, T. Ando, and T.-h. Kao. Evidence that intragenic recombination contributes to allelic diversity of the S-RNAase gene at the self-incompatibility (S) locus in Petunia inflata. Plant Physiol. 125:1012-1022.

Fasano, J.M., S.J. Swanson, E.B. Blancaflor, P.E. Down, T.-h. Kao, and S. Gilroy. Changes in root cap pH are required for the gravity response of the Arabidopsis root. Plant Cell. 13:907-921.

Skirpan, A.L., A.G. McCubbin, T. Ishimizu, X. Wang, Y. Hu, P.E. Dowd, H. Ma, and T.-h. Kao. Isolation and characterization of kinase interacting protein 1, a pollen protein that interacts with the kinase domain of PRK1, a receptor-like kinase of petunia. Plant Physiol. 126:1480-1492.

Luscher, B., and C.A. Keller. Ubiquitination, proteasomes and GABA-A receptors. Nature Cell Biol. 3:232-233.

Luscher, B., and J.-M. Fritschy. Subcellular localization and regulation of GABAA receptors and associated proteins. Intern. Rev. Neurobiol. 48:31-64.

Urtishak, S.L., E. McKenna, and A.M. Mastro. Prolactin and prolactin receptor expression in rat, small intestine, intraepithelial lymphocytes during neonatal development. Develop. Immunol. 8:319-330.

Ahluwalia, N., A.M. Mastro, R. Ball, M.P. Miles, G. Handte, and R. Rajendra. Cytokine production by stimulated mononuclear cells did not change with aging in apparently healthy, well-nourished women. Mech. Ageing Dev. 122:1269-1279.

Dohi K., A.M. Mastro, M.P. Miles, J.A. Bush, D.S. Grove, S.K. Leach, J.S. Volek, B.C. Nindl, J.O. Marx, L.A. Gotshalk, M. Putukian, W.J. Sebastianelli, and W.J. Kreamer. Lymphocyte proliferation in response to acute heavy resistance exercise in women: Influence of muscle strength and total work. Eur. J. Appl. Physiol. 85:367-373.

Kerber, B., I. Monge, M. Mueller, P.J. Mitchell, and S.M. Cohen. The Drosophia homologue of the AP-2 transcription factor is required for joint formation and cell survival during leg development. Development. 128:1231-1238.

Monge, I., R. Krishnamurthy, D. Sims, F. Hirth, M. Spenglier, L. Kammermeir, H. Reichert, and P.J. Mitchell. Drosophila transcription factor AP-2 in proboscis, leg and brain central complex development. Development. 128:1239-1252.

Stewart, H.J., A. Brennan, M. Rahman, G. Zoidl, P.J. Mitchell, K.R. Jessen, and R. Mirsky. Developmental regulation and overexpression of the transcription factor AP-2, a potential regulator of the timing of Schwann cell generation. Eur. J. Neurosci. 14:363-72.

Spear, E.D., and D.T. W.Ng. The unfolded protein response: No longer just a special teams player. Traffic. 2:515-523.

Ng, D.T.W. Interorganellar signal transduction: The arrest of secretion response. Dev. Cell. 1:319-320.

Vashist, S., W. Kim, W. Belden, E.D. Spear, C. Barlowe, and D.T.W. Ng. Distinct retrieval and retention mechanisms are required for the quality control of endoplasmic reticulum protein folding. J. Cell Biol. 155:355-367.

Meyer, M., S. Park, L. Zeringue, M. Staley, M. McKinstry, R.I. Kaufman, H. Zhang, D. Yan, N. Yennawar, H. Yennawar, G.K. Farber, and B.T. Nixon. A dimeric two-component receiver domain inhibits the σ54-dependent ATPase in DctD. FASEB J. 7:1326-1328.

Prabhu, K.S., V.R. Padala, E. Gumpricht, G. Hildenbrandt, R.W. Scholz, L.M. Sordillo, and C.C. Reddy. Microsomal glutathione S-transferase A1-1 with gluthathione peroxidase activity from sheep liver: Molecular cloning, expression and characterization. Biochem. J. 360:345-354.

Pugh, B.F. The RNA polymerase II transcription machinery. In: Transcription Factors. (J. Locker, ed.), pp. 1-16, BIOS Scientific Publishers, Oxford.

Pugh, B.F., and D. Gilmour. Genome-wide analysis of protein-DNA interactions in living cells. Genome Biol. 2:1013.1-1013.3.

Stitzel, M.L., R. Durso, and J.C. Reese. The proteasome regulates the UV-induced activation of the AP-1 like transcription factor Gcn4. Genes Dev. 15:128-133.

Reese, J.C., and M.R. Green. Genetic analysis of yeast TAF68 reveals multiple links to the cell cycle. Yeast 18:1197-1205.

Li, B., and J.C. Reese. Ssn6-Tup1 regulates RNR3 by positioning nucleosomes and affecting the chromatin structure at the URS. J. Biol. Chem. 276:33788-337897.

Hassan, A.H., K.E. Neely, M. Vignali, J.C. Reese, and J.L. Workman. Promoter targeting of chromatin-modifying complexes. Frontiers Biosci. 6:1054-1064.

Durso, R.J., A.K. Fisher, T.J. Albright-Frey, and J.C. Reese. Analysis of TAF90 mutants displaying allele-specific and global defects in transcription. Mol. Cell. Biol. 21:7331-7344.

Williamson, P., S. van den Eijnde, and R.A. Schlegel. Phosphatidylserine exposure and phagocytosis of apoptotic cells. Methods Cell Biol. 65:339-365.

Schlegel, R.A., and P. Williamson. Phosphatidylserine, a death knell. Cell Death Differ. 8:551-563.

Williamson, P., A. Christie, T. Kohlin, R.A. Schlegel, P. Comfurius, M. Harmsma, R.F.A. Zwaal, and E.M. Bevers. Phospholipid scramblase activation pathways in lymphocytes. Biochemistry. 40:8065-8072.

Williamson, P., and R.A. Schlegel. Of umbrellas, jazz and slow-steppin’. Cell Death Differ. 8:104-105.

Gavin, I.M., M.P. Kladde, and R.T. Simpson. Tup1p represses Mcm1p transcriptional activiation and chromatin remodeling of an a-cell-specific gene. EMBO J. 19:5875-5883.

Wang, X., and R.T. Simpson. Chromatin structure mapping in Sacharomyces cerevisiae in vivo with Dnase I. Nucleic Acids Res. 29:1943-1950.

Tan, S. A modular polycistronic expression system for overexpressing protein complexes in E. coli. Prot. Expr. Purif. 21:224-234.

Brown, C.E., L. Howe, K. Sousa, S.C. Alley, M.J. Carrozza, S. Tan, and J.L. Workman. Recruitment of HAT complexes by director activator interactions with the ATM-related Tra1 subunit. Science. 292:2333-2337.

Selleck, W., R. Howley, Q. Fang, V. Podolny, M.G. Fried, S. Buratowksi, and S. Tan. Histone fold complexes within yeast TFIID transcriptional coactivator. Nature Struct. Biol. 8:695-700.

Tan, S. One HAT size fits all? Nature Struc. Biol. 8:8-10.

Thomas, G.H. Spectrin: The ghost in the machine. BioEssays. 23:152-160.

Mester, T., and M. Tien. Engineering of a manganese-binding site in lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. Biochem. Bioph. Res. Comm. 284:723-728.

Mester, T., and M. Tien. Oxidation mechanism of ligninolytic enzymes involved in the degradation of environmental pollutants. Inter. Biodet. Biodeg. 46:51-59.

Cheng, H., T. Tchaikovskaya, Y.-S.L. Tu, J. Chapman, B. Qian, W.-M. Ching, M. Tien, J.D. Rowe, Y.V. Patskovsky, I. Listowsky, and C.-P.D. Tu. Rat glutathione S-transferase M4-4: An isoenzyme with unique structural features including a redox-reactive cysteine-115 residue that forms mixed disulphides with glutathione. Biochem. J. 356:403-414.

Mester, T., K. Ambert-Balay, S. Ciofi-Baffoni, L. Banci, A.D. Jones, and M. Tien. Oxidation of a tetrameric nonphenolic lignin model compound by lignin peroxidase. J. Biol. Chem. 276:22985-22990.

Cheng, H., T. Tchaikovskaya, Y.-S.L. Tu, J. Chapman, B. Qian, W.-M. Ching, M. Tien, J.D. Rowe, Y.V. Patskovsky, I. Listowsky, and C.-P.D. Tu. Rat glutathione S-transferase M4-4: An isoenzyme with unique structural features including a redox-reactive cysteine-115 residue that forms mixed disulphides with glutathione. Biochem. J. 356:403-414.

Hassan, A.H., K.E. Neely, and J.L. Workman. Histone acetyltransferase complexes stabilize SWI/SNF binding to promoter nucleosomes. Cell. 104:817-827.

Brown, C.E., L. Howe, K. Sousa, S.C. Alley, S. Tan, and J.L. Workman. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science. 292: 2333-2337.

Hassan, A.H., K.E. Neely, M. Vignali, J.C. Reese, and J.L. Workman. Promoter targeting of chromatin-modifying complexes. Frontiers Biosci. 6:1054-1064.

Howe, L., D. Austin, P. Grant, S. John, R.G. Cook, J.L. Workman, and L. Pillus. Histone H3 specific HATs are essential for cell cycle progression. Genes Dev. 15:3144-3154.

Osada, S., A. Sutton, N. Muster, C.E. Brown, J.R. Yates, R. Sternglanz, and J.L. Workman. The yeast SAS (something about silencing) protein complex contains a MYST-type acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 15:3155-3168.