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1998 Faculty Publications

Abmayr, S.M. and C.A. Keller. Drosophila myogenesis, and insights into the role of nautilus. Curr. Topics Dev. Biol. 38:35-80.

Keller, C.A., M.A. Grill, and S.M. Abmayr. A role for nautilus in the differentiation of muscle precursors. Dev. Biol. 202:157-171.

Hansen, D. and P. Babitzke. trp RNA-binding attenuation protein-mediated long distance RNA refolding regulates translation of trpE in Bacillus subtilis. J. Biol. Chem. 273:20494-20503.

Granger, L., E.B. O'Hara, R. Wang, F.V. Meffen, K. Armstrong, S.D. Yancey, P. Babitzke, and S.R. Kushner. The Escherichia coli mrsC gene is required for cell growth and mRNA decay. J. Bacteriol. 180:1920-1928.

Zeljka, K., P. Babitzke, and E. Hoffman. Myotonic dystrophy: Molecular windows on a complex etiology. Nucleic Acids Res. 26:1363-1368.

Bollinger, J.M.,Jr., C. Krebs, A. Vicol, S. Chen, B.A. Ley, D.E. Edmondson, and B.H. Huynh. Engineering the diiron site of Escherichia coli ribonucleotide reductase protein R2 to accumulate an intermediate similar to Hperoxo, the putative peroxodiiron(III) complex from the methane monooxygenase catalytic cycle. J. Am. Chem. Soc. 120:1094-1095.

Huynh, B.H., J.M. Bollinger, Jr., and D.E. Edmondson. Reaction intermediates in oxygen activation by enzymes containing carboxylate-bridged binuclear iron clusters. In: Spectroscopic Methods in Bioinorganic Chemistry. (E. I. Solomon and K. O. Hodgson, eds.), pp. 403-422, American Chemical Society, Washington, D.C.

Moënne-Loccoz, P., J. Baldwin, B.A. Ley, T.M. Loehr, and J.M. Bollinger, Jr. O₂ activation by non-heme diiron proteins: Identification of a symmetric µ-1,2-peroxide in a mutant of ribonucleotide reductase. Biochemistry 37:14659-14663.

Parkin, S.E., S. Chen, B.A. Ley, L. Mangravite, D.E. Edmondson, B.H. Huynh, and J.M. Bollinger, Jr. Electron injection through a specific pathway determines the outcome of oxygen activation at the diiron cluster in the F208Y mutant of Escherichia coli ribonucleotide reductase protein R2. Biochemistry 37:1124-1130.

Chung, S., G. Shen, J.G. Ormerod, and D.A. Bryant. Insertional inactivation studies of the csmA and csmC genes of the green sulfur bacterium Chlorobium vibrioforme 8327: The chlorosome protein CsmA is required for viability but CsmC is dispensable. FEMS Microbiol. Lett. 164:353-361.

Gruber, T.M. and D.A. Bryant. An overview of sigma factors of RNA polymerase in phototrophic bacteria. In: The Phototrophic Prokaryotes. (G.A. Peschek, W. Löffelhardt, and G. Schmetterer, eds.), pp. 791-798, Plenum, Vienna.

Gruber, T.M. and D.A. Bryant. Characterization of the alternative sigma factors SigD and SigE in Synechococcus sp. strain PCC 7002. SigE is implicated in transcription of post-exponential-phase-specific genes. Arch. Microbiol. 169:211-219.

Gruber, T.M. and D.A. Bryant. Characterization of the group 1 and group 2 sigma factors of the green sulfur bacterium Chlorobium tepidum and the green gliding bacterium Chloroflexus aurantiacus. Arch. Microbiol. 170:285-296.

Gruber, T.M., J.A. Eisen, K. Gish, and D.A. Bryant. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. FEMS Microbiol. Lett. 162:53-60.

Nomura, C. and D.A. Bryant. Cytochrome c6 from Synechococcus sp. PCC 7002. In: The Phototrophic Prokaryotes, (G. A. Peschek, W. Löffelhardt, and G. Schmetterer, eds.), pp. 269-274. Plenum, Vienna.

Sakamoto, T. and D.A. Bryant. Growth at low temperature causes nitrogen limitation in the cyanobacterium Synechococcus sp. PCC 7002. Arch. Microbiol. 169:10-19.

Sakamoto, T., V.B. Delgaizo, and D.A. Bryant. Growth on urea can trigger peroxidative death of the cyanobacterium Synechococcus sp. strain PCC 7002. Appl. Envir. Microbiol. 64:2361-2366.

Sakamoto, T., G. Shen, S. Higashi, N. Murata, and D.A. Bryant. Alteration of low-temperature susceptibility of the cyanobacterium Synechococcus sp. PCC 7002 by genetic manipulation of membrane lipid unsaturation. Arch. Microbiol. 169:20-28.

Xia, Z., R.W. Broadhurst, E.D. Laue, D.A. Bryant, J.H. Golbeck, and D.S. Bendall. Structure and properties of PsaD in solution. Eur. J. Biochem. 255:309-316.

Yang, F., G. Shen, W.M. Schluchter, B. Zybailov, A. Ganago, D.A. Bryant, and J.H. Golbeck. Deletion of the PsaF polypeptide modifies the environment of the redox-active phylloquinone (A1). Evidence for unidirectionality of electron transfer in photosystem I. J. Phys. Chem. 102:8288-8299.

Yang, F., G. Shen, W.M. Schluchter, B. Zybailov, A. Ganago, J.H. Golbeck, and D.A. Bryant. Structural and functional analyses of cyanobacterial photosystem I: The directionality of electron transfer. In: The Phototrophic Prokaryotes. (G.A. Peschek, W. Löffelhardt, and G. Schmetterer, eds.), pp. 21-33. Plenum, Vienna.

Zhao, J., R. Li, and D.A. Bryant. Measurement of Photosystem I activity by photoreduction of recombinant flavodoxin. Anal. Biochem. 264:263-270.

Farber, G.K. Sensing photons. Nature Struct. Biol. 5:415-418.

Staley, M., L.C. Zeringue, R.D. Kidd, G.K. Farber, and B.T. Nixon. Crystallization and characterization of the Rhizobium meliloti DctD two-component receiver domain. Acta Cryst. D54:1416-1418.

Teo, B., R.D., Kidd, J. Mack, A. Tiwari, D. Hernandez, A.T. Phillips, and G.K. Farber. Crystallization and preliminary x-ray studies of Pseudomonas putida histidine ammonia-lyase. Acta Cryst. D54:681-683.

Becker, D.F., U. Leartsakulpanich, K.K. Surerus, J.G. Ferry, and S.W. Ragsdale. Electrochemical and spectroscopic properties of the iron-sulfur flavoprotein from Methanosarcina thermophila. J. Biol. Chem. 273:26462-26469.

Maupin-Furlow, J.A., H.C. Aldrich, and J.G. Ferry. Biochemical characterization of the 20S proteasome from the methanoarchaeaon Methanosarcina thermophila. J. Bacteriol. 180:1480-1487.

Singh-Wissmann, K., C. Ingram-Smith, R.D. Miles, and J.G. Ferry. Identification of essential glutamates in the acetate kinase from Methanosarcina thermophila. J. Bacteriol. 180:1129-1134.

Frisque, R.J. Rearranged and chimaeric primate polyomavirus genomes. Dev. Biol. Stand. 94:103-113.

Levine, A., J. Butel, K. Dorries, J. Goedert, R. Frisque, R. Garcea, A. Morris, F. O'Neill, and K. Shah. SV40 as a putative human commensal. Dev. Biol. Stand. 94:245-269.

Newman, J.S., and R.J. Frisque. Identification of SV40 in brain, kidney and urine of healthy and SIV-infected rhesus monkeys. J. Neurovirol. 4:394-406.

Hunter, S.J., C.V. Gay, P.A. Osdosy, and L.L. Peters. Spectrin localization in osteoclasts: Immunocytochemistry, cloning and partial sequencing. J. Cell. Biochem. 71:204-215.

Praul, C.A., K.D. Brubaker, R.M. Leach, and C.V. Gay. Detection of endogenous biotin-containing proteins in bone and cartilage cells with streptavidin systems. Biochem. Biophy. Res. Comm. 247:312-314.

Reginato, A.M., R.I. Bashey, G. Rosselot, R.M. Leach, C.V. Gay, and S.A. Jimenez. Type X collagen biosynthesis and expression in avian tibial dyschondroplasia. Osteoarthr. Cartilage 6:125-136.

Stains, J.P., and C.V. Gay. Asymmetric distribution of functional sodium-calcium exchanger in primary osteoblasts. J. Bone Miner. Res. 13:1862-1869.

Benjamin, L.R., and D.S. Gilmour. Nucleosomes are not necessary for promoter-proximal pausing in vitro on the Drosophila hsp70 promoter. Nucleic Acids Res. 26:1051-1055.

Golbeck, J.H. Comparison of in vitro and in vivo mutants of PsaC in Photosystem I: Protocols for mutagenesis and techniques for analysis. In: Methods in Enzymol.: Photosynthesis: Molecular Biology of Energy Capture (L. McIntosh, ed.) 297:95—123, Academic Press Inc, San Diego, CA.

Hays, A-M., I.R. Vassiliev, J.H. Golbeck, and R. Debus. Role of D1-His190 in proton coupled electron transfer reactions in Photosystem II: A chemical complementation study. Biochemistry37:11352-11365.

Kjaer, B., N.-U. Frigaard, F. Yang, B. Zybailov, M. Miller, J.H. Golbeck, and H.V. Scheller. Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor, A₁’. Biochemistry 37:3237-3242.

Mamedov, M.D., K.N. Gourovskaya, I.R. Vassiliev, J.H. Golbeck, and A. Yu. Semenov. Electrogenicity accompanies photoreduction of the iron-sulfur clusters F_A and F_B in Photosystem I. FEBS Lett. 431:219-223.

Naver, H., M.P. Scott, J.H. Golbeck, and H.V. Scheller. The eight amino acid internal loop of PSI-C mediates association of low molecular mass iron-sulfur proteins with the P700-F_X core in Photosystem I. J. Biol. Chem. 273:18778-18783.

Vassiliev, I.R., Y.-S. Jung, F. Yang, and J.H. Golbeck. PsaC is oriented with iron-sulfur cluster F_B as the immediate electron donor to ferredoxin and flavodoxin in Photosystem I. Biophys. J.74:2029-2035.

Xia, Z., R.W. Broadhurst, E.D. Laue, B.D. Bryant, J.H. Golbeck, and D.S. Bendall. Structure and properties in solution of PsaD, an extrinsic polypeptide of Photosystem I. Eur. J. Biochem.255:309-316.

Yang, F., G. Shen, W.M. Schluchter, B.L. Zybailov, A.O. Ganago, I. Vassiliev, D.A. Bryant, and J. H. Golbeck. Deletion of the PsaF polypeptide modifies the environment of the redox-active phylloquinone (A₁). Evidence for unidirectionality of electron transfer in Photosystem I. J. Phys. Chem. 102:8288-8299.

Bender, M., A. Reik, J. Close, A. Telling, E. Epner, S. Fiering, R. Hardison, and M. Groudine. Description and targeted deletion of 5’ hypersensitive site 5 and 6 of the mouse-globin locus control region. Blood 92:4394-4403.

Chui, D.H.K., R. Hardison, C. Riemer, W. Miller, M.F.H. Carver, T.P. Molchanova, G.D. Efremov, and T.H.J. Huisman. An electronic database of human hemoglobin variants on the World Wide Web. Blood. 91:2643-2644.

Hardison, R. Hemoglobins from bacteria to man: Evolution of different patterns of gene expression. J. Exp. Biol. 201:1099-1117.

Hardison, R., C. Riemer, D.H.K. Chui, T.H.J. Huisman, and W. Miller. Electronic access to sequence alignments, experimental results, and human mutations as an aid to studying globin gene regulation. Genomics 47:429-437.

Hardison, R.C., D.H.K. Chui, C.R. Riemer, W. Miller, M.F.H. Carver, T.P. Molchanova, G.D. Efremov, and T.H.J. Huisman. Access to a syllabus of human hemoglobin variants (1996) via the World Wide Web. Hemoglobin 22:113-127.

Li, J., C.T. Noguchi, W. Miller, R. Hardison, and A. Schechter. Multiple regulatory elements in the 5' flanking sequence of the human epsilon globin gene. J. Biol. Chem. 273:10202-10209.

Riemer, C., A. El Sherbini, N. Stojanovic, S. Schwartz, P. Kwitkin, W. Miller, and R. Hardison. A database of experimental results on globin gene expression. Genomics 53:325-337.

Shellenberger, K., R. Grindeland, and W.C. Hymer. Rat anterior pituitary hormone cells: responses to variable gravity. Aviat. Space and Environ. Med. 69:37-44.

Marc, J., C.L. Granger, J. Brincat, D.D. Fisher, T.-h. Kao, A.G. McCubbin, and R.J. Cyr. Use of a GFP-MAP4 reporter gene for visualizing cortical microtubule rearrangements in living epidermal cells. Plant Cell 10:1927-1940

Verica, J.A. and T.-h. Kao. Self-incompatibility: Self/nonself discrimination between pollen and pistil. In: Cellular Interaction of Signalling Pathways in Plant Development, (F.L. Schiavo, R.L. Last, G. Morelli, and N.V. Raikhel, eds.) NATO ASI Series, Subseries H, Cell Biology 104:263-273, Springer-Verlag, Berlin, Heidelberg.

Verica, J.A., A.G. McCubbin, and T.-h. Kao. Are the hypervariable regions of S RNases sufficient for allele-specific recognition of pollen? Plant Cell 10:314-316.

van Huizen, R., K. Miller, D.-M. Chen, Y. Li, Z.-C. Lai, R.W. Raab, W.S. Stark, R.D. Shortridge, and M. Li. Two distinctly positioned PDZ domains mediate multivalent INAD-phospholipae C interactions essential for G protein-coupled signaling. EMBO J. 17:2285-2297.

Miles, M.P., S.K. Leach, W.J. Kraemer, K. Dohi, J.A. Bush, and A.M. Mastro. Leukocyte adhesion molecule expression during intense resistance exercise. J. Appl. Phys. 85:1604-1609.

N.T. Triplett-McBride, A.M. Mastro, J.M. McBride, J.A. Bush, M. Putukian, W.J. Sebastianelli, and W.J. Kraemer. Plasma proenkephalin peptide F and human B cell responses to exercise stress in fit and unfit women. Peptides 19:731-738.

Staley, M., L.C. Zeringue, R.D. Kidd, B.T. Nixon, and G.K. Farber. Crystallization and preliminary X-ray studies of the Rhizobium meliloti DctD two-component receiver domain. Acta Cryst. D54:1416 — 1418.

Teo, B., R.D. Kidd, J. Mack, A. Tiwari, D. Hernandez, A.T. Phillips, and G.K. Farber. Crystallization and preliminary x-ray studies of Pseudomonas putida histidine ammonia-lyase. Acta Cryst. D54:681-683.

Carlini, L.E., U. Curth, B. Kindler, C. Urbanke, and R.D. Porter. Identification of amino acids stabilizing the tetramerization of the single-stranded DNA-binding protein of Escheridchia coli. FEBS Lett. 430:197-200.

Chicca, J.J., D. Auble, and B.F. Pugh. Cloning and biochemical characterization of TAF-172, a human homologue of yeast Mot1. Mol. Cell. Biol. 18:1701-1710.

Grant, P.A., D. Schieltz, M.G. Pray-Grant, D.J. Steger, J.C. Reese, J. Yates, and J.L. Workman. A subset of TAF_IIs are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94:45-53.

Halleck, M.S., D. Pradhan, C. Blackman, C. Berkes, P. Williamson, and R. A. Schlegel. Multiple members a third subfamily of P-type ATPases identified by genomic and EST sequences. Genome Res. 8:354-361.

Schlegel, R.A., S. Krahling, A.J. Christie, and P. Williamson. Phosphatidylserine as a signal for recognition and phagocytosis: The proteins involved. In: Choline, Phospholipids, Health and Disease. (B. F. Szuhaj and S. Zeisel, eds), pp. 57-68. American Oil Chemists Society Press, Champaign, IL.

Steitz, M., J. Wickenheisser, and E. Siegfried. Over-expression of Zeste white 3 blocks Wingless signaling in the Drosophila embryonic midgut. Dev. Biol. 197:218-233.

Patterton, H.G., C.C. Landel, D. Landsman, C.L. Peterson, and R.T. Simpson. The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae. J. Biol. Chem. 273, 7268-7276.

Xu, M., R.T. Simpson, and M.P. Kladde. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Mol. Cell. Biol. 18:1201-1212.

Wu, C., K. Weiss, C. Yang, M.A. Harris, B.-K. Tye, C.S. Newlon, R.T. Simpson, and J.E. Haber. Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching. Genes Dev. 12:1726-1737.

Weiss, K., and R.T. Simpson. High resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLalpha. Mol. Cell. Biol. 18: 5392-5403.

Kladde, M.P., and R.T. Simpson. Rapid detection of functional expression of C-5-DNA methyltransferases in yeast. Nucleic Acids Res 26:1354-1355.

Xu, M., M.P. Kladde, J.L. Van Etten, and R.T. Simpson. Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC. Nucleic Acids Res. 26:3961-3967.

Simpson, R.T. Chromatin structure and analysis of mechanisms of activators and repressors. Methods 15:283-94.

Thomas, G.H., D.C. Zarnescu, A.E. Juedes, M.A. Bales, A. Londergan, C.C. Korte, and D.P. Kiehart. Drosophila $_Heavy-spectrin is essential for development and contributes to specific cell fates in the eye. Development 125:2125-2134.

Thomas, G.H. Molecular evolution of spectrin repeats. Bioessays 20:600.

Tan, S., and T.J. Richmond. Crystal structure of the yeast MAT2/MCM1/DNA ternary complex. Nature 391:660-666.

Tan, S., and T.J. Richmond. Eukaryotic transcription factors. Curr. Opin. Struct. Biol. 8:41-48.

Ambert-Balay, K., S.M. Fuchs, and M. Tien. Identification of the veratryl alcohol binding site in lignin peroxidase by site-directed mutagenesis. Biochem. Biophys. Res. Commun. 251:283-286.

Banci, L., I. Bertini, L. dal Pozzo, R. del Conte, and M. Tien. Monitoring the role of oxalate in manganese peroxidase. Biochemistry 37:9009-9015.

Zapanta, L.S., T. Hattori, M. Rzetskaya, and M. Tien. The cloning of Phanerochaete chrysosporium leu2 by complementation of bacterial auxotrophs and transformation of fungal auxotrophs. Appl. Environ. Microbiol. 64:2624-2629.

Barlev, N.A., V. Poltoratsky, T. Owen-Hughes, C. Ying, L. Liu, J.L. Workman, and S.L. Berger. Repression of GCN5 histone acetyltransferase activity via bromodomain-mediated binding and phosphorylation by the Ku-DNA-dependent protein kinase complex. Mol. Cell. Biol. 18:1349-1358.

Côté, J., C.L. Peterson, and J.L. Workman. Perturbation of nucleosome structure by the SWI/SNF complex persists following its detachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. USA. 9:4947-4952.

Eberharter, A., S. John. P.A. Grant, R.T. Utley, and J.L. Workman. Identification and analysis of yeast nucleosomal histone acetyltransferase complexes. Methods 15:315-321.

Grant, P.A., D. Schieltz, M.G. Pray-Grant, J.R. Yates III, and J.L. Workman. The ATM-related cofactor Tra1 is a component of the purified SAGA complex. Mol. Cell 2:863-867.

Grant, P.A., and J.L. Workman. Transcription: A lesson in sharing (news and views). Nature 396:410-411.

Grant, P.A., D. Schieltz, M.G. Pray-Grant, D.J. Steger, J.C. Reese, J.R. Yates III, and J.L. Workman. A subset of TBP-associated factors, TAF_IIs, are integral components of the SAGA complex that are required for nucleosome acetylation and transcription stimulation. Cell 94:45-53.

Grant, P.A., D.E. Sterner, L.J. Duggan, J.L. Workman, and S.L. Berger. The SAGA unfolds: convergence of transcription regulators in chromatin modifying complexes. Trends Cell Biol. 8:193-197.

John, S., and J.L. Workman. Bookmarking genes for activation on condensed mitotic chromosomes. Bioessays 20:275-279.

John, S., and J.L. Workman. Just the facts of chromatin transcription (perspective). Science 282:1836-1837.

Mutskov, V., D. Gerber, D. Angelov, J. Ausio, J.L. Workman, and S. Dimitrov. Persistent interactions of the core histone tails with nucleosomal DNA following acetylation and transcription factor binding. Mol.Cell. Biol. 18:6298-6304.

Steger, D.J., A. Eberharter, S. John, P.A. Grant, and J.L. Workman. Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. USA. 95:12924-12929.

Utley, R.T., K. Ikeda, P.A. Grant, J. Côté, D.J. Steger, A. Eberharter, S. John, and J.L. Workman. Transcriptional activators target histone acetyltransferase complexes to nucleosomes. Nature 394:498-502.

Vignali, M., and J.L. Workman. Location and function of linker histones (review). Nature Struct. Biol. 5:1025-1028.

Workman, J.L., Editor, Chromatin Function in Transcription. Methods: A Companion to Methods in Enzymology. Academic Press, Harcourt Brace & Company, San Diego, CA

Workman, J.L., and Kingston, R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Ann. Rev. Biochem. 67:549-579.