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2000 Faculty Publications

Bour, B.A, M. Chakravarti, J. West, and S.M. Abmayr. Drosophila SNS, a member of the immunoglobulin superfamily that is essential for myoblast fusion. Genes Dev. 14:1498-1511.

Yakhnin, A.V., J.J. Trimble, C.R. Chiaro, and P. Babitzke. Effects of mutations in the L-tryptophan binding pocket of the trp RNA-binding attenuation protein of Bacillus subtilis. J. Biol. Chem. 275:4519-4524.

Du, H., A.V. Yakhnin, S. Dharmaraj, and P. Babitzke. trp RNA-binding attenuation protein (TRAP)-5’ stem-loop RNA interaction is required for proper transcription attenuation control of the Bacillus subtilis trpEDCFBA operon. J. Bacteriol. 182:1819-1827.

Voegtli, W.C., N. Khidekel, J. Baldwin, B.A. Ley, J.M. Bollinger, Jr., and A.C. Rosenzweig. Crystal structure of the ribonucleotide reductase R2 mutant that accumulates a µ-1,2-peroxodiiron(III) intermediate during oxygen activation. J. Am. Chem. Soc. 122:3255-3261.

Krebs, C., R. Davydov, J. Baldwin, B.M. Hoffman, J.M. Bollinger, Jr., and B.H. Huynh. Mössbauer and EPR characterization of the S = 9/2 mixed-valence Fe(II)Fe(III) cluster in cryoreduced R2 subunit of Escherichia coli ribonucleotide reductase. J. Am. Chem. Soc. 122:5327-5336.

Yang, Y.-S., J. Baldwin, B.A. Ley, J.M. Bollinger, Jr., and E.I. Solomon. Spectroscopic and electronic structure description of the reduced binuclear non-heme iron active site in ribonucleotide reductase from E. coli: Comparison to reduced D9 desaturase and electronic structure contributions to differences in O2 reactivity. J. Am. Chem. Soc. 122:8495-8510.

Baldwin, J., C. Krebs, B.A. Ley, B.H. Huynh, and J.M. Bollinger, Jr. Mechanism of rapid electron transfer during oxygen activation in the R2 subunit of Escherichia coli ribonucleotide reductase. 1. Evidence for a transient tryptophan radical. J. Am. Chem. Soc. 122:12195-12206.

Krebs, C., S. Chen, J. Baldwin, B.A. Ley, U. Patel, D.E. Edmondson, B.H. Huynh, and J.M. Bollinger, Jr. Mechanism of rapid electron transfer during oxygen activation in the R2 subunit of Escherichia coli ribonucleotide reductase. 2. Evidence for and consequences of blocked electron transfer in the W48F variant. J. Am. Chem. Soc. 122:12207-12219.

Cosper, N.J., S. Booker, F.J. Ruczicka, P.A. Frey, and R.A. Scott. Direct FeS cluster involvement in generation of a radical in lysine 2,3-aminomutase. Biochemistry 39:15668-15673.

Wu, W., S. Booker, K.W. Lieder, V. Bandarian, G.H. Reed, and P.A. Frey. Lysine 2,3-aminomutase and (E)--4,5-didehydrolysine: Characterization of an allylic analog of a substrate-based radical in the catalytic mechanism. Biochemistry 39:9561-9570.

Brenchley, J.E. Putting microorganisms to work. In: Many Faces Many Microbes: Personal reflection in microbiology. (R. Atlas, ed.), pp. 219-225, ASM Press, Washington, DC.

Sheridan, P. and J.E. Brenchley. Characterization of a salt tolerant family 42 ß-galactosidase from a psychrophilic Antarctic Planococcus isolate. Appl. Environ. Microbiol. 66:2438-2444.

Sheridan, P., N. Panasik, J. Coombs, and J.E. Brenchley. Approaches to deciphering the structural basis of low temperature enzyme activity. Biochem. Biophys. Acta 1543:413-429.

Panasik, N., J.E. Brenchley, and G. Farber. Distribution of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases. Biochem. Biophys. Acta 1543:189-201.

Moore, G.L., C.D. Maranas, K.R. Gutshall, and J.E. Brenchley. Modeling and optimization of DNA recombination. Comp. Chem. Eng. 24:693-699.

Johnson, W., G. Shen, B. Zybailov, D. Kolling, R. Reategui, S. Beauparlant, I.R.Vassiliev, D.A. Bryant, A.D. Jones, J.H. Golbeck, and P. Chitnis. Mutagenesis of the menA and menB genes in the biosynthetic pathway to phylloquinone in Synechocystis sp. PCC 6803. I. Recruitment of a foreign quinone into the A₁ site of photosystem I. J. Biol. Chem. 275:8523-8530.

Antonkine, M.L., D. Bentrop, I. Bertini, C. Luchinat, G. Shen, D.A. Bryant, D. Stehlik, and J.H. Golbeck. Paramagnetic ¹H NMR spectroscopy of the reduced unbound Photosystem I subunit PsaC: sequence specific assignment of contact shifted resonances and identification of mixed and equal valence Fe-Fe pairs in [4Fe-4S] centers FA- and FB-. J. Bioinorg. Chem. 5:381-392.

Bhaya, D., N.R. Bianco, D.A. Bryant, and A.R. Grossman. Type IV pilus biogenesis and motility in the cyanobacterium Synechocystis sp. PCC 6803. Mol. Microbiol. 37:941-951.

Vassilieva, E.V., N.-U. Frigaard, and D.A. Bryant. Chlorosomes: the light-harvesting antennae of green bacteria. The Spectrum 13:7-13.

Arnold, J.J. and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): assembly of stable, elongation-competent complexes by using a symmetrical primer/template substrate (sym/sub). J. Biol. Chem. 275:5329-5336.

Gohara, D.W., S. Crotty, J.J. Arnold, J.D.Yoder, R. Andino, and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): Structural, biochemical and biological analysis of conserved structural motifs A and B. J. Biol. Chem. 275:25523-25532.

Zhong, W., E. Ferrari, C. Lesburg, D. Maag, S.K.B. Ghosh, C.E. Cameron, J.Y.N. Lau, and Z. Hong. Template/primer requirements and single nucleotide incorporation by Hepatitis C virus nonstructural protein 5B polymerase. J. Virol. 74:9134-9143.

Crotty, S., D. Maag, J.J. Arnold, W. Zhong, J.N.Y. Lau, Z. Hong, R. Andino, and C.E. Cameron. The broad-spectrum antiviral ribonucleoside, ribavirin, is a RNA virus mutagen. Nature Medicine 6:1375-1379.

Borup, B. and J.G. Ferry. O-Acetylserine sulfhydrylase from Methanosarcina thermophila. J. Bacteriol. 182:45-50.

Liermann, L.L., B.E. Kalinowski, S.L. Brantley, and J.G. Ferry. Role of bacterial siderophores in dissolution of horneblende. Geochem. Cosmochem. Acta 64:587-602.

Singh-Wissmann, K., R.D. Miles, C. Ingram-Smith, and J.G. Ferry. Identification of essential arginines in the acetate kinase from Methanosarcina thermophila. Biochemistry 39:3671-3677.

Tripp, B.C. and J.G. Ferry. A structure-function study of a proton transport pathway in the gamma-class carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39:9232-9240.

Iverson, T.M., B.E. Alber, C. Kisker, J.G. Ferry, and D.C. Rees. A closer look at the active site of g-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 39:9222-9231.

Borup, B. and J.G. Ferry. Cysteine biosynthesis in the Archaea: Methanosarcina thermophila utilizes O-acetylserine sulfhydrylase. FEMS Microbiol. Lett. 189:205-210.

Smith, K.S. and J.G. Ferry. Procaryotic carbonic anhydrases. FEMS Microbiol. Rev. 24:335-366.

Leartsakulpanich, U., M.L. Antonkine, and J.G. Ferry. Site-specific mutational analysis of a novel cysteine motif proposed to ligate the 4Fe-4S cluster in the iron-sulfur flavoprotein (Isf) of the thermophilic methanoarchaeon Methanosarcina thermophila. J. Bacteriol. 182:5309-5316.

Ingram-Smith, C., R.D. Barber, and J.G. Ferry. The role of histidines in the acetate kinase from Methanosarcina thermophila. J. Biol. Chem. 275:33765-33700.

Smith, K.S., N.J. Cosper, C. Stalhandske, R.A. Scott, and J.G. Ferry. Structural and kinetic characterization of an archaeal b class carbonic anhydrase. J. Bacteriol. 182:6605-6613.

Chatterjee, M., T.B. Weyandt, and R.J. Frisque. Identification of archetype and rearranged forms of BK virus in leukocytes from healthy individuals. J. Med. Virol. 60:353-362.

Bollag, B., C. Prins, E.L. Snyder, and R.J. Frisque. Purified JC virus T and T’ proteins differentially interact with the retinoblastoma family of tumor suppressor proteins. Virology 274:165-178.

Armen, T. and C.V. Gay. Simultaneous detection and functional response of testosterone and estradial receptors in osteoblast plasma membranes. J. Cell Biochem. 79:620-627.

Gay, C.V., V.R. Gilman, and T. Sugiyama. Perspectives on osteoblast and osteoclast function. Poultry Sci. 79:1005-1009.

Luan, Y., C.A. Praul, and C.V. Gay. Confocal imaging and timing of secretion of matrix proteins by osteoblasts derived from avian long bone. Comp. Biochem. Physiol. 126:213-221.

[Multi-authored, C.V. Gay] Proposed standard nomenclature for new tumor necrosis factor family members involved in the regulation of bone resorption. J. Bone Min. Res. 15:2293-2296.

Tang, H., Y. Liu, L. Madabusi, and D.S. Gilmour. Promoter proximal pausing on the hsp70 promoter in Drosophila depends upon the upstream regulator. Mol. Cell. Biol. 20:2569-2580.

Shenkarev, V., I. Vassiliev, and J.H. Golbeck. A kinetic assessment of the sequence of electron transfer from F_X to F_A and further to F_B in Photosystem I. The value of the equilibrium constant between F_X and F_A. Biophys. J. 78:363-372.

Johnson, W.T., G. Shen, B. Zybailov, D. Kolling, R. Reategui, S. Beauparlant, I.R. Vassiliev, D.A. Bryant, A.D. Jones, J.H. Golbeck, and P. Chitnis. Recruitment of a foreign quinone into the A₁ site of Photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. PCC 6803. J. Biol. Chem. 275:8523-8530.

Zybailov, B., A. van der Est, S.G. Zech, C. Teutloff, W.T. Johnson, G. Shen, R. Bittl, D. Stehlik, P. Chitnis, and J.H. Golbeck. Recruitment of a foreign quinone into the A₁ site of Photosystem I. II. Structural and functional characterization of phylloquinone biosynthetic pathway mutants by EPR and ENDOR spectroscopy. J. Biol. Chem. 275:8531-8539.

Semenov, A.Y., I.R. Vassiliev, A. van der Est, M.D. Mamedov, B. Zybailov, G. Shen, D. Stehlik, B.A. Diner, P.R. Chitnis, and J.H. Golbeck. Recruitment of a foreign quinone into the A₁ site of Photosystem I. III. Altered kinetics of electron transfer in phylloquinone biosynthetic pathway mutants studied by time-resolved optical, EPR and electrometric techniques. J. Biol. Chem. 275:23429-23438.

Vassiliev, I.R., M.T. Ronan, G. Hauska, and J.H. Golbeck. Photoreduction of the bound iron-sulfur clusters in green sulfur bacteria: Resolution of the g-tensor for the electron acceptor F_X in Chlorobium tepidum. Biophys. J. 78:363-372.

Antonkine, M., D. Bentrop, I. Bertini, D.A. Bryant, C. Luchinat, G. Shen, D. Stehlik, and J.H. Golbeck. Paramagnetic ¹H NMR spectroscopy of the reduced, unbound Photosystem I subunit PsaC: Sequence specific assignment of contact-shifted resonances and identification of mixed and equal valence Fe-Fe pairs in [4Fe-4S] centers F_A and F_B. J. Biol. Inorg. Chem. 5:381-392.

Ikonomi, P., C. T. Noguchi, W. Miller, H. Kassahun, R. C. Hardison, and A. Schecter. Levels of GATA1/GATA2 transcription factors modulate expression of embryonic and fetal hemoglobins. Gene 261:277-287.

Schwartz, S., Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R.C. Hardison, and W. Miller. PipMaker — A web server for aligning two genomic DNA sequences. Genome Res. 10:577-586.

Florea, L., M. Li, C. Riemer, B. Giardine, W. Miller, and R.C. Hardison. Validating computer programs for functional genomics in gene regulatory regions. Curr. Genomics 1:11-27.

Hardison, R.C. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16:369-372.

Bulger, M., M.A. Bender, J. Hjikke van Doorninck, B. Wertman, C. Farrell, G. Felsenfeld, M. Groudine, and R.C. Hardison. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters. Proc. Natl. Acad. Sci. USA 97:14560-14565.

Dowd, P.E., A.G. McCubbin, X. Wang, J.A. Verica, T. Tsukamoto, T. Ando, and T.-h. Kao. Use of Petunia inflata as a model for the study of solanaceous type self-incompatibility. Ann. Bot. 85 (Suppl. A):87-93.

McCubbin, A.G., X. Wang, and T.-h. Kao. Identification of self-incompatibility (S-) locus linked pollen cDNA markers in Petunia inflata. Genome 43:619-627.

McCubbin, A.G., C. Zuniga, and T.-h. Kao. Construction of a binary artificial chromosome library of Petunia inflata and the identification of large genomic fragments linked to the self-incompatibility (S-) locus. Genome 43:820-826.

McCubbin, A.G. and T.-h. Kao. Molecular recognition and response in pollen and pistil interactions. Annu. Rev. Cell. Dev. Biol. 16:333-364.

Kao, T.-h. and A.G. McCubbin. A social stigma. Nature 403:840-841.

Cosgrove, D.J., S. Gilroy, T.-h. Kao, H. Ma, and J.C. Schultz. Meeting Report: Plant Signaling. Cross talk among geneticists, physiologists, and ecologists. Plant Physiol. 124:499-505.

Nguyen, D., M. Rohrbaugh, and Z.-C. Lai. The Drosophila homolog of onecut homeodomain proteins is a neural-specific transcription activator with a potential role in regulating neural differentiation. Mech. Dev. 97:55-70.

Wen, Y., D. Nguyen, Y. Li, and Z.-C. Lai. The N-terminal BTB/POZ domain and C-terminal sequences are essential for Tramtrack69 to specify cell fate in the developing Drosophila eye. Genetics 156:195-203.

Dhulkotia, D., D. Nguyen, and Z.-C. Lai. Evolutionary conservation of a leucine-rich repeat transmembrane protein Gp150 in Drosophila and Bombyx. Dev. Genes Evol. 210:145-150.

Lorez, M., D. Benke, B. Lüscher, H. Mohler, and J.A. Benson. Single-channel properties of neuronal GABA_A-receptors lacking the g2 subunit. J. Physiol. 527:11-31.

Baer, K., C. Essrich, S. Balsiger, M.J. Wick, R.A. Harris, J.-M. Fritschy, and B. Lüscher. Rescue of g2 subunit-deficient mice by transgenic overexpression of the GABA_A receptor g2S or g2L subunit isoforms. Eur. J. Neurosci. 7:2639-43.

Wick, M.J., R.A. Radcliffe, B.J. Bowers, M.P. Mascia, B. Lüscher, R.A. Harris, and J.M. Wehner. Behavioral changes produced by transgenic expression of g2L and g2S subunits of the GABA_A receptor. Eur. J. Neurosci. 7:2634-2638.

Simonian, S.X., M.J. Skinner, W. Sieghart, C. Essrich, B. Lüscher, and A. Herbison. Role of GABA_A receptor g2 subunit in the development of the gonadotropin-releasing hormone neurons in vivo. Eur. J. Neurosci. 12:3488-3496.

Pazur, J., M. Perlof, A. Frymoyer, C.J.P. Jenson, H. Micolochick, and A.M. Mastro. The isolation and properties of the dimer subunit of concanavalin. Am. J. Protein Chem. 19:353-359.

Bush, J.A., K. Dohi, A.M. Mastro, J.S. Volek, J.M. Lynch, N.T. Triplett-McBride, M. Putukian, W.J. Sebastianelli, R.U. Newton, K. Hakkinen and W.J. Kraemer. Exercise and recovery responses of lymphokines to heavy resistance exercise. J. Strength Cond. Res. 14:344-349.

Miles, M.P., L.T. Mackinnon, D.S. Grove, N.I. Williams, J.A. Bush, J.O. Marx, W.J. Kraemer, and A.M. Mastro. Potential mechanisms of post-exercise suppression of NK cell activity: cell number, perforin mRNA and CD2. The Physiologist 43:360.

Anttila, M.A., J.K. Kellokoski, K.I. Moisio, P.J. Mitchell, S. Saarikoski, K. Syrjanen, and V.M. Kosma. Expression of transcription factor AP-2alpha predicts survival in epithelial ovarian cancer. Br. J. Cancer 82:1974-1983.

Kramer, P.R., R. Krishnamurthy, P.J. Mitchell, and S. Wray. Transcription factor activator protein-2 is required for continued luteinizing hormone-releasing hormone expression in the forebrain of developing mice. Endocrinology 141:1823-1838.

Kramer, P.R., G. Guerrero, R. Krishnamurthy, P.J. Mitchell, and S. Wray. Ectopic expression of luteinizing hormone-releasing hormone and peripherin in the respiratory epithelium of mice lacking transcription factor AP-2alpha. Mech. Dev. 94:79-94.

Karjalainen, J.M., J.K. Kellokoski, A.J. Mannermaa, H.E. Kujala, K.I. Moisio, P.J. Mitchell, M.J. Eskelinen, E.M. Alhava, and V.M. Kosma. Failure in post-transcriptional processing is a possible inactivation mechanism of AP-2alpha in cutaneous melanoma. Br. J. Cancer 82:2015-2021.

Ng, D.T.W., E.D. Spear, and P. Walter. The unfolded protein response pathway regulates multiple aspects of secretory and membrane protein biogenesis and endoplamic reticulum quality control. J. Cell Biol. 150:77-88.

Studholme D.J., M. Buck, and B.T. Nixon. Identification of sigma-N-dependent promoters in bacterial genomes. Microbiology 146:3021-3023.

Pugh, B.F. Control of gene expression through regulation of the TATA binding protein. Gene 255:1-14.

Reese, J.C., Z. Zhang, and H. Kurpad. Identification of a novel TFIID subunit, TSG2/TAF48. J. Biol. Chem. 275:17391-17398.

Li, B. and J.C. Reese. Derepression of DNA damage-regulated genes requires yeast TBP-associated factors. EMBO J. 19:4091-4100.

Callahan, M.K., P. Williamson, and R.A. Schlegel. Surface expression of phosphatidylserine on macrophages is required for phagocytosis of apoptotic thymocytes. Cell Death Differ. 7:645-653.

Schlegel, R.A., M.K. Callahan, and P. Williamson. The central role of phosphatidylserine in the phagocytosis of apoptotic thymocytes. Ann. N. Y. Acad. Sci. 926:217-225.

Ducker, C.E. and R.T. Simpson. The organized chromatin domain of the repressed yeast a cell specific gene STE6 contains two molecules of the corepressor Tup1p per nucleosome. EMBO J. 19:400-409.

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

Tan, S., Y. Hunziker, L. Pellegrini, and T.J. Richmond. Crystallization of the yeast MATalpha2/MCM1/DNA ternary complex: general methods and principles for protein/DNA cocrystallization. J. Mol. Biol. 297:947-959.

Santucci, R., C. Bongiovanni, S. Marini, R. Del Conte, M. Tien, L. Banci, and M. Coletta. Redox equilibria of manganese peroxidase from Phanerochaetes chrysosporium: functional role of residues on the proximal side of the haem pocket. Biochem. J. 349:85-90.

Ambert-Balay, K., M. Dougherty, and M. Tien. Reactivity of manganese peroxidase: site-directed mutagenesis of residues in proximity to the porphyrin ring. Arch. Biochem. Biophys. 382:89-94.

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

Brown, C.E., T. Lechner, L. Howe, and J.L. Workman. The many HATs of transcription coactivators. Trends Biochem. Sci. 25:15-19.

Vignali, M., A.H. Hassan, K.E. Neeley, and J.L. Workman. ATP-dependent chromatin remodeling complexes. Mol. Cell. Biol. 20:1899-1910.

Wallberg, A.E., K.E. Neeley, A.H. Hassan, J.-A. Gustafsson, J.L. Workman, and A.P.H. Wright. Recruitment of the SWI-SNF chromatin remodeling complex as a mechanism of gene activation by the glucocorticoid receptor tau1 activation domain. Mol. Cell. Biol. 20:2004-2013.

John, S., L. Howe, S.T. Travov, P.A. Grant, R. Sternglanz, and J.L. Workman. The something about silencing protein, SAS3, is the catalytic subunit of the NuA3 complex, a TAF30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)/FACT complex. Genes Dev. 14:1196-1208.

Vignali, M., D. Steger, K.E. Neely, and J.L. Workman. Distribution of acetylated histones resulting from Gal4-VP16 recruitment of SAGA and NuA4 complexes. EMBO J. 19:2629-2640.

Peterson, C.L. and J.L. Workman. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10:187-192.

Lechner, T., P.A. Grant, A. Eberharter, D. Vannier, Y. Yu, G. Brosch, D.J. Stillman, D. Shore, and J.L. Workman. Sds3 (Suppressor of defective silencing 3) is an integral component of the yeast Sin3 / Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J. Biol Chem. 275:40961-40966.

Elgin, S.C.R. and J.L. Workman. Frontiers in Molecular Biology Series. Chromatin Structure and Gene Expression, (S.C.R. Elgin and J.L. Workman, eds.) (second edition) 328 p., Oxford University Press, Oxford.

Howe, L., C.E. Brown, T. Lechner, and J.L. Workman. Histone acetyltransferase complexes and their link to transcription. Critical Reviews In: Eukaryotic Gene Expression 9:231-243.

Berger, S.L., P.A. Grant, J.L. Workman, and C.D. Allis. Histone acetyltransferase transcription adaptor complexes. In: Chromatin Structure and Gene Expression. S.C.R. Elgin and J.L.Workman, eds. (second edition), 135-148 p., Oxford University Press, Oxford.