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2004 Faculty Publications

Ades, S.E. Control of the alternative sigma factor σ^E in Escherichia coli. Curr. Opin. Microbiol. 7:157-162.

Ades, S.E. Proteolysis: adaptor, adaptor, catch me a catch. Curr. Biol. 14:R924-R926.

Yakhnin, H., H. Zhang, A.V. Yakhnin, and P. Babitzke. The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding. J. Bacteriol. 186:278-286.

Deikus, G., P. Babitzke, and D.H. Bechhofer. Recycling of a regulatory protein by degradation of the RNA to which it binds. Proc. Natl. Acad. Sci. USA 101:2747-2751.

Babitzke, P. Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Curr. Opin. Microbiol. 7:132-139.

Yakhnin, H. and P. Babitzke. Gene replacement method for determining conditions in which Bacillus subtilis genes are essential or dispensable for cell viability. Appl. Microbiol. Biotechnol. 64:382-386.

Saleh, L., B.A. Kelch, B.A. Pathickal, J. Baldwin, B.A. Ley, and J.M. Bollinger, Jr. Mediation by indole analogues of electron transfer during oxygen activation in variants of Escherichia coli ribonucleotide reductase R2 lacking the electron-shuttling tryptophan 48. Biochemistry 43:5943-5952.

Saleh, L., C. Krebs, B.A. Ley, S. Naik, B.H. Huynh, and J.M. Bollinger, Jr. Use of a chemical trigger for electron transfer to characterize a precursor to cluster X in assembly of the iron-radical cofactor of Escherichia coli ribonucleotide reductase. Biochemistry 43:5953-5964.

Wei, P.-p., A.J. Skulan, N. Mitic, Y.-S. Yang, L. Saleh, J.M. Bollinger, Jr., and E.I. Solomon. Electronic and spectroscopic studies of the non-heme reduced binuclear iron sites of two ribonucleotide reductase variants: comparison to reduced methane monooxygenase and contributions to O₂ reactivity. J. Am. Chem. Soc. 126:3777-3788.

Behshad, E., S.E. Parkin, and J.M. Bollinger, Jr. Mechanism of cysteine desulfurase Slr0387 from Synechocystis sp. PCC 6803: kinetic analysis of cleavage of the persulfide intermediate by chemical reductants. Biochemistry 43:12220-12226.

Tirupati, B., J.L. Vey, C.L. Drennan, and J.M. Bollinger, Jr. Kinetic and structural characterization of Slr0077/SufS, the essential cysteine desulfurase from Synechocystis sp. PCC 6803. Biochemistry 43:12210-12219.

Lu, S., E. Libby, L. Saleh, G. Xing, J.M. Bollinger, Jr., and P. Moenne-Loccoz. Characterization of NO adducts of the diiron center in protein R2 of Escherichia coli ribonucleotide reductase and site-directed variants; implications for the O₂ activation mechanism. J. Biol. Inorg. Chem. 9:818-827.

Skulan, A.J., T.C. Brunold, J. Baldwin, L. Saleh, J.M. Bollinger, Jr., and E.I. Solomon. Nature of the peroxo intermediate of the W48F/D84E ribonucleotide reductase variant: implication for O₂ activation by binuclear non-heme iron enzymes. J. Am. Chem. Soc. 126:8842-8855.

Riggs-Gelasco, P.J., J.C. Price, R.B. Guyer, J.H. Brehm, E.W. Barr, J.M. Bollinger, Jr., and C. Krebs. EXAFS spectroscopic evidence for an Fe=O unit in the Fe(IV) intermediate observed during oxygen activation by Taurine:a-ketoglutarate dioxygenase. J. Am. Chem. Soc. 126:8108-8109.

Iwig, D.F., A.T. Grippe, T.A. McIntyre, and S.J. Booker. Isotope and elemental effects indicate a rate-limiting methyl transfer as the initial step in the reaction catalyzed by Escherichia coli cyclopropane fatty acid synthase. Biochemistry 43:13510-13524.

Iwig, D.F. and S.J. Booker. Insight into the polar reactivity of the onium chalcogen analogues of S-adenosyl-L-methionine. Biochemistry 43:13496-13509.

Cicchillo, R.M., K.-H. Lee, C. Baleanu-Gogonea, N.M. Nesbitt, C. Krebs, and S.J. Booker. Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per polypeptide. Biochemistry 43:11770-11781.

Cicchillo, R.M., M.A. Baker, E.J. Schnitzer, E.B. Newman, C. Krebs, and S.J. Booker. Escherichia coli L-serine deaminase requires a [4Fe-4S] cluster in catalysis. J. Biol. Chem. 279:32418-32425.

Cicchillo, R.M., D.F. Iwig, A.D. Jones, N.M. Nesbitt, C. Baleanu-Gogonea, M.G. Souder, L. Tu, and S.J. Booker. Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to synthesize one equivalent of lipoic acid. Biochemistry 43:6378-6386.

Booker, S.J. Unraveling the pathway of lipoic acid biosynthesis. Chem. Biol. 11:10-12.

Miteva, V.I., P.P. Sheridan, and J.E. Brenchley. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl. Environ. Microbiol. 70:202-213.

Frigaard, N.-U., Y. Sakuragi, and D.A. Bryant. Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation. In: Photosynthesis Research Protocols. (R. Carpentier, ed.), pp. 325-340, Humana Press, Totowa, NJ.

Frigaard, N.-U., H. Li, K.J. Milks, and D.A. Bryant. Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. J. Bacteriol. 186:646-653.

Wang, T., G. Shen, R. Balasubramanian, L. McIntosh, D.A. Bryant, and J.H. Golbeck. The sufR gene (sll0088 in Synechocystis sp. Strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria. J. Bacteriol. 186:956-967.

van der Est, A., A.I. Valieva, Y.E. Kandrashkin, G. Shen, D.A. Bryant, and J.H. Golbeck. Removal of PsaF alters forward electron transfer in Photosystem I: Evidence for fast reoxidation of Q_K-A in subunit deletion mutants of Synechococcus sp. PCC 7002. Biochemistry 43:1264-1275.

Maresca, J.A., A. Gomez Maqueo Chew, M.R. Ponsatí, N.-U. Frigaard, J.G. Ormerod, and D.A. Bryant. The bchU gene of Chlorobium tepidum encodes the C-20 methyltransferase in bacteriochlorophyll c biosynthesis. J. Bacteriol. 186:2558-2566.

Frigaard, N.-U., J.A. Maresca, C.E. Yunker, A.D. Jones, and D.A. Bryant. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J. Bacteriol. 186:5210-5220.

Frigaard, N.-U. and D.A. Bryant. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch. Microbiol. 182:265-276.

Arnold, J.J. and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg²⁺. Biochemistry 43:5126-5137.

Arnold, J.J., D.W. Gohara, and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn²⁺. Biochemistry 43:5138-5148.

Gohara, D.W., J.J. Arnold, and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): kinetic, thermodynamic, and structural analysis of ribonucleotide selection. Biochemistry 43:5149-5158.

de Miranda, J.R., M. Drebot, S. Tyler, M. Shen, C.E. Cameron, D.B. Stoltz, and S.M. Camazine. Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus. J. Gen. Virol. 85:2263-2270.

Huang, L., E.V. Sineva, M.R.S. Hargittai, S.D. Sharma, M. Suthar, K.D. Raney, and C.E. Cameron. Purification and characterization of hepatitis C virus non-structural protein 5A expressed in Escherichia coli. Protein Expr. Purif. 37:144-153.

Graci, J.D. and C.E. Cameron. Challenges for the development of ribonucleoside analogues as inducers of error catastrophe. Antivir. Chem. Chemother. 15:1-13.

Freistadt, M.S., G.D. Meades, and C.E. Cameron. Lethal mutagens: broad-spectrum antivirals with limited potential for development of resistance? Drug Resist. Update 7:19-24.

Ding, Y.-H.R. and J.G. Ferry. Flavin mononucleotide-binding flavoprotein family in the domain Archaea. J. Bacteriol. 186:90-97.

Tripp, B.C., C.B. Bell III, F. Cruz, C. Krebs, and J.G. Ferry. A role for iron in an ancient carbonic anhydrase. J. Biol. Chem. 279:6683-6687.

Iyer, P.P., S.H. Lawrence, K.B. Luther, K.R. Rajashankar, H.P. Yennawar, J.G. Ferry, and H. Schindelin. Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila. Structure 12:559-567.

Innocenti, A., S. Zimmerman, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the zinc and cobalt g-class enzyme from the archaeon Methanosarcina thermophila with anions. Bioorg. Med. Chem. Lett. 14:3327-3331.

Innocenti, A., S. Zimmerman, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the beta-class enzyme from the methanoarchaeon Methanobacterium thermoautotrophicum (Cab) with anions. Bioorg. Med. Chem. Lett. 14:4563-4567.

Zimmerman, S., A. Innocenti, A. Casini, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the prokariotic beta and gamma-class enzymes from Archaea with sulfonamides. Bioorg. Med. Chem. Lett. 14:6001-6006.

Parisi, G., M. Perales. M.S. Fornasari, A. Colaneri, N. González-Schain, D. Gómez-Casati, S. Zimmerman, A. Brennicke, A. Araya, J.G. Ferry, J. Echave, and E. Zabaleta. Gamma carbonic anhydrases in plant mitochondria. Plant Mol. Biol. 55:193-207.

Ziegler, K., T. Bui, R.J. Frisque, A. Grandinetti, and V.R. Nerurkar. A rapid in vitro polyomavirus DNA replication assay. J. Virol. Methods 122:123-127.

Frisque, R.J., C. Hofstetter, and S.K. Tyagarajan. Transforming activities of JC virus early proteins. In: Polyomaviruses and Human Diseases. (N. Ahsan, ed.), pp. 1-22, Landes Bioscience, Georgetown, TX.

Mastro, A.M., C.V. Gay, D.R. Welch, H.J. Donahue, J. Jewell, R. Mercer, D. DiGirolamo, E.M. Chislock, and K. Guttridge. Breast cancer cells induce osteoblast apoptosis: a possible contributor to bone degradation. J. Cell. Biochem. 91:265-276.

Harms, J.F., D R. Welch, R.S. Samant, L.A. Shevde, M.E. Miele, G.R. Babu, S F. Goldberg, V.R. Gilman, D.M. Sosnowski, D.A. Campo, C.V. Gay, L.R. Budgeon, R. Mercer, J. Jewell, A.M. Mastro, H.J. Donahue, N. Erin, M.T. Debies, W.J. Meehan, A.L. Jones, G. Mbalaviele, A. Nickols, N.D. Christensen, R. Melly, L.N. Beck, J. Kent, R.K. Rader, J.J. Kotyk, M.D. Pagel, W.F. Westlin, and D.W. Griggs. A small molecule antagonist of the avß3 integrin suppresses MDA-MB-435 skeletal metastasis. Clin. Exp. Metast. 21:119-128.

Zhang, Z., C.-H. Wu, and D.S. Gilmour. Analysis of polymerase II elongation complexes by native gel electrophoresis: Evidence for a novel carboxyl-terminal domain-mediated termination mechanism. J. Biol. Chem. 279:23223-23228.

van der Est, A., A.I. Valieva, Y.E. Kandrashkin, G. Shen, D.A. Bryant, and J.H. Golbeck. Removal of PsaF alters forward electron transfer in Photosystem I: Evidence for fast reoxidation of Q_K-A in subunit deletion mutants of Synechococcus sp. PCC 7002. Biochemistry 43:1264-1275.

Wang, T., G. Shen, R. Balasubramanian, L. McIntosh, D.A. Bryant, and J.H. Golbeck. The sufR gene (sll0088 in Synechocystis sp. Strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria. J. Bacteriol. 186:956-967.

Cohen, R.O., G. Shen, J.H. Golbeck, W. Xu, P.R. Chitnis, A.I. Valieva, A. van der Est, Y. Pushkar, and D. Stehlik. Evidence for asymmetric electron transfer in cyanobacterial photosystem I: analysis of a methionine-to-leucine mutation of the ligand to the primary electron acceptor A₀. Biochemistry 43:4741-4754.

Pushkar, Y.N., J.H. Golbeck, D. Stehlik, and H. Zimmerman. Asymmetric hydrogen-bonding of the quinine cofactor in photosystem I probed by ¹³C-labeled naphthoquinones. J. Phys. Chem. B 108:9439-9448.

Golbeck, J.H., M.L. Antonkine, and D. Stehlik. Breaking biological symmetry in membrane proteins: how PsaC evolved to orient asymmetrically on the photosystem I core. Cell. Mol. Biol. Lett. 9:24-28.

Antonkine, M.L. and J.H. Golbeck. Photosystem I: F_X, F_A, and F_B iron-sulfur clusters. In: Encyclopedia of Biological Chemistry. (W. J. Lennarz and D. M. Lane, eds.), pp. 348-356, Elsevier, Amsterdam.

Ovcharenko, I., G.G. Loots, R.C. Hardison, W. Miller, and L. Stubbs. zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14:472-477.

Hardison, R.C., F. Chiaromonte, D. Kolbe, H. Wang, H. Petrykowska, L. Elnitski, S. Yang, B. Giardine, Y. Zhang, C. Riemer, S. Schwartz, D. Haussler, K.M. Roskin, R.J. Weber, M. Diekhans, W.J. Kent, M.J. Weiss, J. Welch, and W. Miller. Global predictions and tests of erythroid regulatory regions. In: Cold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII, “The Genome of Homo sapiens.” (B. Stillman, D. Stewart, and J. Ebert, eds.), pp. 335-344, Cold Spring Harbor Press, Cold Spring Harbor, NY.

Gibbs, R.A., G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, P.E. Burch, G. Okwuonu, S. Hines, L. Lewis, C. DeRamo, O. Delgado, S. Dugan-Rocha, G. Miner, M. Morgan, A. Hawes, R. Gill, R.A. Holt, M.D. Adams, P.G. Amanatides, H. Baden-Tillson, M. Barnstead, S. Chin, C.A. Evans, S. Ferriera, C. Fosler, A. Glodek, Z. Gu, D. Jennings, C.L. Kraft, T. Nguyen, C.M. Pfannkoch, C. Sitter, G.G. Sutton, J.C. Venter, T. Woodage, D. Smith, H.M. Lee, E. Gustafson, P. Cahill, A. Kana, L. Doucette-Stamm, K. Weinstock, K. Fechtel, R.B. Weiss, D.M. Dunn, E.D. Green, R.W. Blakesley, G.G. Bouffard, P.J. De Jong, K. Osoegawa, B. Zhu, M. Marra, J. Schein, I. Bosdet, C. Fjell, S. Jones, M. Krzywinski, C. Mathewson, A. Siddiqui, N. Wye, J. McPherson, S. Zhao, C.M. Fraser, J. Shetty, S. Shatsman, K. Geer, Y. Chen, S. Abramzon, W.C. Nierman, P.H. Havlak, R. Chen, K.J. Durbin, A. Egan, Y. Ren, X.Z. Song, B. Li, Y. Liu, X. Qin, S. Cawley, K.C. Worley, A.J. Cooney, L.M. D'Souza, K. Martin, J.Q. Wu, M.L. Gonzalez-Garay, A.R. Jackson, K.J. Kalafus, M.P. McLeod, A. Milosavljevic, D. Virk, A. Volkov, D.A. Wheeler, Z. Zhang, J.A. Bailey, E.E. Eichler, E. Tuzun, E. Birney, E. Mongin, A. Ureta-Vidal, C. Woodwark, E. Zdobnov, P. Bork, M. Suyama, D. Torrents, M. Alexandersson, B.J. Trask, J.M. Young, H. Huang, H. Wang, H. Xing, S. Daniels, D. Gietzen, J. Schmidt, K. Stevens, U. Vitt, J. Wingrove, F. Camara, M. Mar Alba, J.F. Abril, R. Guigo, A. Smit, I. Dubchak, E.M. Rubin, O. Couronne, A. Poliakov, N. Hubner, D. Ganten, C. Goesele, O. Hummel, T. Kreitler, Y.A. Lee, J. Monti, H. Schulz, H. Zimdahl, H. Himmelbauer, H. Lehrach, H.J. Jacob, S. Bromberg, J. Gullings-Handley, M.I. Jensen-Seaman, A.E. Kwitek, J. Lazar, D. Pasko, P.J. Tonellato, S. Twigger, C.P. Ponting, J.M. Duarte, S. Rice, L. Goodstadt, S.A. Beatson, R.D. Emes, E.E. Winter, C. Webber, P. Brandt, G. Nyakatura, M. Adetobi, F. Chiaromonte, L. Elnitski, P. Eswara, R.C. Hardison, M. Hou, D. Kolbe, K. Makova, W. Miller, A. Nekrutenko, C. Riemer, S. Schwartz, J. Taylor, S. Yang, Y. Zhang, K. Lindpaintner, T.D. Andrews, M. Caccamo, M. Clamp, L. Clarke, V. Curwen, R. Durbin, E. Eyras, S.M. Searle, G.M. Cooper, S. Batzoglou, M. Brudno, A. Sidow, E.A. Stone, J.C. Venter, B.A. Payseur, G. Bourque, C. Lopez-Otin, X.S. Puente, K. Chakrabarti, S. Chatterji, C. Dewey, L. Pachter, N. Bray, V.B. Yap, A. Caspi, G. Tesler, P.A. Pevzner, D. Haussler, K.M. Roskin, R. Baertsch, H. Clawson, T.S. Furey, A.S. Hinrichs, D. Karolchik, W.J. Kent, K.R. Rosenbloom, H. Trumbower, M. Weirauch, D.N. Cooper, P.D. Stenson, B. Ma, M. Brent, M. Arumugam, D. Shteynberg, R.R. Copley, M.S. Taylor, H. Riethman, U. Mudunuri, J. Peterson, M. Guyer, A. Felsenfeld, S. Old, S. Mockrin, and F. Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.

Yang, S., A.F. Smit, S. Schwartz, F. Chiaromonte, K.M. Roskin, D. Haussler, W. Miller, and R.C. Hardison. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 14:517-527.

Tufarelli, C., R. Hardison, W. Miller, J. Hughes, K. Clark, N. Ventress, A.M. Frischauf, and D.R. Higgs. Comparative analysis of the a-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res. 14: 623-630.

Kolbe, D., J. Taylor, L. Elnitski, P. Eswara, J. Li, W. Miller, R. Hardison, and F. Chiaromonte. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 14:700-707.

Miller, W., K.D. Makova, A. Nekrutenko, and R.C. Hardison. Comparative Genomics. Annu. Rev. Genomics Hum. Genet. 5:15-56.

Welch, J.J., J.A. Watts, C.R. Vakoc, Y. Yao, H. Wang, R.C. Hardison, G.A. Blobel, L.A. Chodosh, and M.J. Weiss. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104:3136-3147.

Feingold, E.A., P.J. Good, M. Guyer, S. Kamholz, L. Liefer, K. Wetterstrand, F.S. Collins, T.R. Gingeras, D. Kampa, E.A. Sekinger, J. Cheng, H. Hirsch, S. Ghosh, Z. Zhu, S. Patel, A. Piccolboni, A. Yang, H. Tammana, S. Bekiranov, P. Kapranov, G. Church, K. Struhl, R. Harrison, B. Ren, T.H. Kim, L.O. Barrera, C. Qu, S. Van Calcar, R. Luna, C.K. Glass, M.G. Rosenfeld, R. Guigo, S. Antonarakis, E. Birney, M. Brent, L. Pachter, A. Reymond, M. Dermitzakis, C. Dewey, D. Keefe, F. Denoeud, J. Lagarde, J. Ashurst, T. Hubbard, J.J. Wesselink, R. Castelo, E. Eyras, R.M. Myers, A. Sidow, S. Batzoglou, N.D. Trinklein, S.J. Hartman, S.F. Aldred, E. Anton, D.I. Schroeder, S.S. Marticke, L. Nguyen, J. Schmutz, J. Grimwood, M. Dickson, G.M. Cooper, E.A. Stone, G. Asimenos, M. Brudno, A. Dutta, N. Karnani, C.M. Taylor, H.K. Kim, G. Robins, G. Stamatoyannopoulos, J.A. Stamatoyannopoulos, M. Dorschner, P. Sabo, M. Hawrylycz, R. Humbert, J. Wallace, M. Yu, P. Navas, M. Olson, M. McArthur, W.S. Noble, I. Dunham, C.M. Koch, R.M. Andrews, G.K. Clelland, S. Wilcox, J.M. Fowler, K.D. James, P. Groth, O.M. Dovey, P.D. Ellis, V.L. Wraight, A.J. Mungall, P. Dhami, H. Fiegler, C.F. Langford, N.P. Carter, D. Vetrie, M. Snyder, G. Euskirchen, A. Urban, U. Nagalakshmi, J. Rinn, G. Popescu, P. Bertone, J. Rozowsky, O. Emanuelsson, T. Royce, S. Chung, M. Gerstein, Z. Lian, J. Lian, Y. Nakayama, S. Weissman, V. Stolc, W. Tongprasit, H. Sethi, S. Jones, M. Marra, H. Shin, J. Schein, M. Clamp, K. Lindblad-Toh, J. Chang, D.B. Jaffe, M. Kamal, E.S. Lander, T. Mikkelson, J. Vinson, M.C. Zody, P.J. de Jong, K. Osoegawa, M. Nefedov, B. Zhu, T.J. Vasicek, D. Zhou, S. Luo, A.D. Baxevanis, T.G. Wolfsberg, I.E. Holt, F.S. Collins, G.E. Crawford, J. Whittle, E.D. Green, G.G. Bouffard, E.H. Margulies, M.E. Portnoy, N.F. Hansen, P.J. Thomas, J.C. McDowell, B. Maskeri, A.C. Young, J.R. Idol, R.W. Blakesley, G. Schuler, W. Miller, R. Hardison, L. Elnitski, P. Shah, S.L. Salzberg, M. Pertea, W.H. Majoros, D. Haussler, D. Thomas, K. Rosenbloom, H. Clawson, A. Siepel, W.J. Kent, Z. Weng, S. Jin, A. Halees, H. Burden, U. Karaoz, Y. Fu, Y. Yu, C. Ding, C.R. Cantor, R.E. Kingston, J. Dennis, R.D. Green, M.A. Singer, T.A. Richmond, J.E. Norton, P.J. Farnham, M.J. Oberley, D.R. Inman, M.R. McCormick, H. Kim, C.L. Middle, M.C. Pirrung, X. D. Fu, Y.S. Kwon, Z. Ye, J. Dekker, T.M. Tabuchi, N. Gheldof, J. Dostie, and S.C. Harvey. The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306:636-640.

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Romero, H.M., B.S. Berlett, P.J. Jensen, E.J. Pell, and M. Tien. Investigations into the role of the plastidial peptide methionine sulfoxide reductase in response to oxidative stress in Arabidopsis. Plant Physiol. 136:3784-3794.

Akgül, B. and C.-P. D. Tu. Pentobarbital-mediated regulation of alternative polyadenylation in Drosophila glutathione S-transferase D21 mRNAs. J. Biol. Chem. 279:4027-4033.

Iyer, P.P., S.H. Lawrence, K.B. Luther, K.R. Rajashankar, H.P. Yennawar, J.G. Ferry, and H. Schindelin. Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila. Structure 12:559-567.

Lalrempuia, R., H. Yennawar, Y.A. Mozharivskyj, and M.R. Kollipara. Synthesis, characterization and molecular structures of allenylidene, vinylidene-alkylidene complexes containing [CpOs(PPh₃)₂]⁺ fragment. J. Organomet. Chem. 689:539-543.

Govindaswamy, P., H.P. Yennawar, and M.R. Kollipara. Synthesis, characterization and molecular structure of the [(h⁶-C₆Me₆)Ru( m-N₃)(N₃)]₂ complex and its reactions with some monodentate ligands. J. Organomet. Chem. 689:3108-3112.


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About Us Faculty Facilities Seminars Publications News and Events Outreach Links	About Us 2004 Faculty Publications Ades, S.E. Control of the alternative sigma factor σ^E in Escherichia coli. Curr. Opin. Microbiol. 7:157-162. Ades, S.E. Proteolysis: adaptor, adaptor, catch me a catch. Curr. Biol. 14:R924-R926. Yakhnin, H., H. Zhang, A.V. Yakhnin, and P. Babitzke. The trp RNA-binding attenuation protein of Bacillus subtilis regulates translation of the tryptophan transport gene trpP (yhaG) by blocking ribosome binding. J. Bacteriol. 186:278-286. Deikus, G., P. Babitzke, and D.H. Bechhofer. Recycling of a regulatory protein by degradation of the RNA to which it binds. Proc. Natl. Acad. Sci. USA 101:2747-2751. Babitzke, P. Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. Curr. Opin. Microbiol. 7:132-139. Yakhnin, H. and P. Babitzke. Gene replacement method for determining conditions in which Bacillus subtilis genes are essential or dispensable for cell viability. Appl. Microbiol. Biotechnol. 64:382-386. Saleh, L., B.A. Kelch, B.A. Pathickal, J. Baldwin, B.A. Ley, and J.M. Bollinger, Jr. Mediation by indole analogues of electron transfer during oxygen activation in variants of Escherichia coli ribonucleotide reductase R2 lacking the electron-shuttling tryptophan 48. Biochemistry 43:5943-5952. Saleh, L., C. Krebs, B.A. Ley, S. Naik, B.H. Huynh, and J.M. Bollinger, Jr. Use of a chemical trigger for electron transfer to characterize a precursor to cluster X in assembly of the iron-radical cofactor of Escherichia coli ribonucleotide reductase. Biochemistry 43:5953-5964. Wei, P.-p., A.J. Skulan, N. Mitic, Y.-S. Yang, L. Saleh, J.M. Bollinger, Jr., and E.I. Solomon. Electronic and spectroscopic studies of the non-heme reduced binuclear iron sites of two ribonucleotide reductase variants: comparison to reduced methane monooxygenase and contributions to O₂ reactivity. J. Am. Chem. Soc. 126:3777-3788. Behshad, E., S.E. Parkin, and J.M. Bollinger, Jr. Mechanism of cysteine desulfurase Slr0387 from Synechocystis sp. PCC 6803: kinetic analysis of cleavage of the persulfide intermediate by chemical reductants. Biochemistry 43:12220-12226. Tirupati, B., J.L. Vey, C.L. Drennan, and J.M. Bollinger, Jr. Kinetic and structural characterization of Slr0077/SufS, the essential cysteine desulfurase from Synechocystis sp. PCC 6803. Biochemistry 43:12210-12219. Lu, S., E. Libby, L. Saleh, G. Xing, J.M. Bollinger, Jr., and P. Moenne-Loccoz. Characterization of NO adducts of the diiron center in protein R2 of Escherichia coli ribonucleotide reductase and site-directed variants; implications for the O₂ activation mechanism. J. Biol. Inorg. Chem. 9:818-827. Skulan, A.J., T.C. Brunold, J. Baldwin, L. Saleh, J.M. Bollinger, Jr., and E.I. Solomon. Nature of the peroxo intermediate of the W48F/D84E ribonucleotide reductase variant: implication for O₂ activation by binuclear non-heme iron enzymes. J. Am. Chem. Soc. 126:8842-8855. Riggs-Gelasco, P.J., J.C. Price, R.B. Guyer, J.H. Brehm, E.W. Barr, J.M. Bollinger, Jr., and C. Krebs. EXAFS spectroscopic evidence for an Fe=O unit in the Fe(IV) intermediate observed during oxygen activation by Taurine:a-ketoglutarate dioxygenase. J. Am. Chem. Soc. 126:8108-8109. Iwig, D.F., A.T. Grippe, T.A. McIntyre, and S.J. Booker. Isotope and elemental effects indicate a rate-limiting methyl transfer as the initial step in the reaction catalyzed by Escherichia coli cyclopropane fatty acid synthase. Biochemistry 43:13510-13524. Iwig, D.F. and S.J. Booker. Insight into the polar reactivity of the onium chalcogen analogues of S-adenosyl-L-methionine. Biochemistry 43:13496-13509. Cicchillo, R.M., K.-H. Lee, C. Baleanu-Gogonea, N.M. Nesbitt, C. Krebs, and S.J. Booker. Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per polypeptide. Biochemistry 43:11770-11781. Cicchillo, R.M., M.A. Baker, E.J. Schnitzer, E.B. Newman, C. Krebs, and S.J. Booker. Escherichia coli L-serine deaminase requires a [4Fe-4S] cluster in catalysis. J. Biol. Chem. 279:32418-32425. Cicchillo, R.M., D.F. Iwig, A.D. Jones, N.M. Nesbitt, C. Baleanu-Gogonea, M.G. Souder, L. Tu, and S.J. Booker. Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to synthesize one equivalent of lipoic acid. Biochemistry 43:6378-6386. Booker, S.J. Unraveling the pathway of lipoic acid biosynthesis. Chem. Biol. 11:10-12. Miteva, V.I., P.P. Sheridan, and J.E. Brenchley. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl. Environ. Microbiol. 70:202-213. Frigaard, N.-U., Y. Sakuragi, and D.A. Bryant. Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation. In: Photosynthesis Research Protocols. (R. Carpentier, ed.), pp. 325-340, Humana Press, Totowa, NJ. Frigaard, N.-U., H. Li, K.J. Milks, and D.A. Bryant. Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. J. Bacteriol. 186:646-653. Wang, T., G. Shen, R. Balasubramanian, L. McIntosh, D.A. Bryant, and J.H. Golbeck. The sufR gene (sll0088 in Synechocystis sp. Strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria. J. Bacteriol. 186:956-967. van der Est, A., A.I. Valieva, Y.E. Kandrashkin, G. Shen, D.A. Bryant, and J.H. Golbeck. Removal of PsaF alters forward electron transfer in Photosystem I: Evidence for fast reoxidation of Q_K-A in subunit deletion mutants of Synechococcus sp. PCC 7002. Biochemistry 43:1264-1275. Maresca, J.A., A. Gomez Maqueo Chew, M.R. Ponsatí, N.-U. Frigaard, J.G. Ormerod, and D.A. Bryant. The bchU gene of Chlorobium tepidum encodes the C-20 methyltransferase in bacteriochlorophyll c biosynthesis. J. Bacteriol. 186:2558-2566. Frigaard, N.-U., J.A. Maresca, C.E. Yunker, A.D. Jones, and D.A. Bryant. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J. Bacteriol. 186:5210-5220. Frigaard, N.-U. and D.A. Bryant. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch. Microbiol. 182:265-276. Arnold, J.J. and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg²⁺. Biochemistry 43:5126-5137. Arnold, J.J., D.W. Gohara, and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn²⁺. Biochemistry 43:5138-5148. Gohara, D.W., J.J. Arnold, and C.E. Cameron. Poliovirus RNA-dependent RNA polymerase (3D^pol): kinetic, thermodynamic, and structural analysis of ribonucleotide selection. Biochemistry 43:5149-5158. de Miranda, J.R., M. Drebot, S. Tyler, M. Shen, C.E. Cameron, D.B. Stoltz, and S.M. Camazine. Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus. J. Gen. Virol. 85:2263-2270. Huang, L., E.V. Sineva, M.R.S. Hargittai, S.D. Sharma, M. Suthar, K.D. Raney, and C.E. Cameron. Purification and characterization of hepatitis C virus non-structural protein 5A expressed in Escherichia coli. Protein Expr. Purif. 37:144-153. Graci, J.D. and C.E. Cameron. Challenges for the development of ribonucleoside analogues as inducers of error catastrophe. Antivir. Chem. Chemother. 15:1-13. Freistadt, M.S., G.D. Meades, and C.E. Cameron. Lethal mutagens: broad-spectrum antivirals with limited potential for development of resistance? Drug Resist. Update 7:19-24. Ding, Y.-H.R. and J.G. Ferry. Flavin mononucleotide-binding flavoprotein family in the domain Archaea. J. Bacteriol. 186:90-97. Tripp, B.C., C.B. Bell III, F. Cruz, C. Krebs, and J.G. Ferry. A role for iron in an ancient carbonic anhydrase. J. Biol. Chem. 279:6683-6687. Iyer, P.P., S.H. Lawrence, K.B. Luther, K.R. Rajashankar, H.P. Yennawar, J.G. Ferry, and H. Schindelin. Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila. Structure 12:559-567. Innocenti, A., S. Zimmerman, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the zinc and cobalt g-class enzyme from the archaeon Methanosarcina thermophila with anions. Bioorg. Med. Chem. Lett. 14:3327-3331. Innocenti, A., S. Zimmerman, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the beta-class enzyme from the methanoarchaeon Methanobacterium thermoautotrophicum (Cab) with anions. Bioorg. Med. Chem. Lett. 14:4563-4567. Zimmerman, S., A. Innocenti, A. Casini, J.G. Ferry, A. Scozzafava, and C.T. Supuran. Carbonic anhydrase inhibitors. Inhibition of the prokariotic beta and gamma-class enzymes from Archaea with sulfonamides. Bioorg. Med. Chem. Lett. 14:6001-6006. Parisi, G., M. Perales. M.S. Fornasari, A. Colaneri, N. González-Schain, D. Gómez-Casati, S. Zimmerman, A. Brennicke, A. Araya, J.G. Ferry, J. Echave, and E. Zabaleta. Gamma carbonic anhydrases in plant mitochondria. Plant Mol. Biol. 55:193-207. Ziegler, K., T. Bui, R.J. Frisque, A. Grandinetti, and V.R. Nerurkar. A rapid in vitro polyomavirus DNA replication assay. J. Virol. Methods 122:123-127. Frisque, R.J., C. Hofstetter, and S.K. Tyagarajan. Transforming activities of JC virus early proteins. In: Polyomaviruses and Human Diseases. (N. Ahsan, ed.), pp. 1-22, Landes Bioscience, Georgetown, TX. Mastro, A.M., C.V. Gay, D.R. Welch, H.J. Donahue, J. Jewell, R. Mercer, D. DiGirolamo, E.M. Chislock, and K. Guttridge. Breast cancer cells induce osteoblast apoptosis: a possible contributor to bone degradation. J. Cell. Biochem. 91:265-276. Harms, J.F., D R. Welch, R.S. Samant, L.A. Shevde, M.E. Miele, G.R. Babu, S F. Goldberg, V.R. Gilman, D.M. Sosnowski, D.A. Campo, C.V. Gay, L.R. Budgeon, R. Mercer, J. Jewell, A.M. Mastro, H.J. Donahue, N. Erin, M.T. Debies, W.J. Meehan, A.L. Jones, G. Mbalaviele, A. Nickols, N.D. Christensen, R. Melly, L.N. Beck, J. Kent, R.K. Rader, J.J. Kotyk, M.D. Pagel, W.F. Westlin, and D.W. Griggs. A small molecule antagonist of the avß3 integrin suppresses MDA-MB-435 skeletal metastasis. Clin. Exp. Metast. 21:119-128. Zhang, Z., C.-H. Wu, and D.S. Gilmour. Analysis of polymerase II elongation complexes by native gel electrophoresis: Evidence for a novel carboxyl-terminal domain-mediated termination mechanism. J. Biol. Chem. 279:23223-23228. van der Est, A., A.I. Valieva, Y.E. Kandrashkin, G. Shen, D.A. Bryant, and J.H. Golbeck. Removal of PsaF alters forward electron transfer in Photosystem I: Evidence for fast reoxidation of Q_K-A in subunit deletion mutants of Synechococcus sp. PCC 7002. Biochemistry 43:1264-1275. Wang, T., G. Shen, R. Balasubramanian, L. McIntosh, D.A. Bryant, and J.H. Golbeck. The sufR gene (sll0088 in Synechocystis sp. Strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria. J. Bacteriol. 186:956-967. Cohen, R.O., G. Shen, J.H. Golbeck, W. Xu, P.R. Chitnis, A.I. Valieva, A. van der Est, Y. Pushkar, and D. Stehlik. Evidence for asymmetric electron transfer in cyanobacterial photosystem I: analysis of a methionine-to-leucine mutation of the ligand to the primary electron acceptor A₀. Biochemistry 43:4741-4754. Pushkar, Y.N., J.H. Golbeck, D. Stehlik, and H. Zimmerman. Asymmetric hydrogen-bonding of the quinine cofactor in photosystem I probed by ¹³C-labeled naphthoquinones. J. Phys. Chem. B 108:9439-9448. Golbeck, J.H., M.L. Antonkine, and D. Stehlik. Breaking biological symmetry in membrane proteins: how PsaC evolved to orient asymmetrically on the photosystem I core. Cell. Mol. Biol. Lett. 9:24-28. Antonkine, M.L. and J.H. Golbeck. Photosystem I: F_X, F_A, and F_B iron-sulfur clusters. In: Encyclopedia of Biological Chemistry. (W. J. Lennarz and D. M. Lane, eds.), pp. 348-356, Elsevier, Amsterdam. Ovcharenko, I., G.G. Loots, R.C. Hardison, W. Miller, and L. Stubbs. zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14:472-477. Hardison, R.C., F. Chiaromonte, D. Kolbe, H. Wang, H. Petrykowska, L. Elnitski, S. Yang, B. Giardine, Y. Zhang, C. Riemer, S. Schwartz, D. Haussler, K.M. Roskin, R.J. Weber, M. Diekhans, W.J. Kent, M.J. Weiss, J. Welch, and W. Miller. Global predictions and tests of erythroid regulatory regions. In: Cold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII, “The Genome of Homo sapiens.” (B. Stillman, D. Stewart, and J. Ebert, eds.), pp. 335-344, Cold Spring Harbor Press, Cold Spring Harbor, NY. Gibbs, R.A., G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, P.E. Burch, G. Okwuonu, S. Hines, L. Lewis, C. DeRamo, O. Delgado, S. Dugan-Rocha, G. Miner, M. Morgan, A. Hawes, R. Gill, R.A. Holt, M.D. Adams, P.G. Amanatides, H. Baden-Tillson, M. Barnstead, S. Chin, C.A. Evans, S. Ferriera, C. Fosler, A. Glodek, Z. Gu, D. Jennings, C.L. Kraft, T. Nguyen, C.M. Pfannkoch, C. Sitter, G.G. Sutton, J.C. 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Haussler, K.M. Roskin, R. Baertsch, H. Clawson, T.S. Furey, A.S. Hinrichs, D. Karolchik, W.J. Kent, K.R. Rosenbloom, H. Trumbower, M. Weirauch, D.N. Cooper, P.D. Stenson, B. Ma, M. Brent, M. Arumugam, D. Shteynberg, R.R. Copley, M.S. Taylor, H. Riethman, U. Mudunuri, J. Peterson, M. Guyer, A. Felsenfeld, S. Old, S. Mockrin, and F. Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521. Yang, S., A.F. Smit, S. Schwartz, F. Chiaromonte, K.M. Roskin, D. Haussler, W. Miller, and R.C. Hardison. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 14:517-527. Tufarelli, C., R. Hardison, W. Miller, J. Hughes, K. Clark, N. Ventress, A.M. Frischauf, and D.R. Higgs. Comparative analysis of the a-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res. 14: 623-630. Kolbe, D., J. Taylor, L. Elnitski, P. Eswara, J. Li, W. Miller, R. Hardison, and F. Chiaromonte. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 14:700-707. Miller, W., K.D. Makova, A. Nekrutenko, and R.C. Hardison. Comparative Genomics. Annu. Rev. Genomics Hum. Genet. 5:15-56. Welch, J.J., J.A. Watts, C.R. Vakoc, Y. Yao, H. Wang, R.C. Hardison, G.A. Blobel, L.A. Chodosh, and M.J. Weiss. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104:3136-3147. Feingold, E.A., P.J. Good, M. Guyer, S. Kamholz, L. Liefer, K. Wetterstrand, F.S. Collins, T.R. Gingeras, D. Kampa, E.A. Sekinger, J. Cheng, H. Hirsch, S. Ghosh, Z. Zhu, S. Patel, A. Piccolboni, A. Yang, H. Tammana, S. Bekiranov, P. Kapranov, G. Church, K. Struhl, R. Harrison, B. Ren, T.H. Kim, L.O. Barrera, C. Qu, S. Van Calcar, R. Luna, C.K. Glass, M.G. Rosenfeld, R. Guigo, S. Antonarakis, E. Birney, M. Brent, L. Pachter, A. Reymond, M. Dermitzakis, C. Dewey, D. Keefe, F. Denoeud, J. 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