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Department of Biological Sciences
  Faculty
David A. Shub

Selected Publications
  • Zhao L., Bonocora, R.P., Shub, D.A. and Stoddard, B.L. (2007) The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J. 26:2432-42.
  • Landthaler, M., Shen, B.W., Stoddard, B.L. and Shub, D.A. (2006) I-BasI and I-HmuI: two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities. J. Mol. Biol. 358:1137-1151.
  • Bonocora, R.P. and Shub, D.A. (2004) A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages. J. Bacteriol. 186:8153-8155.
  • Edgell, D.R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M., Li., Z., Boyd, T.M., Shub, D.A. and Belfort, M. (2004) Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor. Nat. Struct. Mol. Biol. 11:936-944.
  • Shen, B.W., Landthaler, M., Shub, D.A. and Stoddard, B.L. (2004) DNA binding and cleavage by the HNH endonuclease I-HmuI. J. Mol. Biol. 342:43-56.
  • Millard, A., Clokie, M.R.J., Shub, D.A. and Mann, N.H. (2004) Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proc. Natl. Acad. Sci. USA 101:11007-11012.
  • Landthaler, M., Lau, N.C. and Shub, D.A. (2004) Group I homing in Bacillus phages SPO1 and SP82: a gene conversion event initiated by a nicking homing endonuclease. J. Bacteriol. 186:4307-4314.
  • Liu, Q., Belle, A., Shub, D.A., Belfort, M. and Edgell, D.R. (2003) SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site. J. Molec. Biol. 334:13-23.
  • Landthaler, M. and Shub, D.A. (2003) The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille. Nucleic Acids Res. 31:3071-3077.
  • Landthaler, M., Begley, U., Lau, N.C., and Shub, D.A. (2002) Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococus aureus phage Twort. Nucleic Acids Res. 30:1935-1943.
  • Belle, A., Landthaler, M., and Shub, D.A. (2002) Intronless Homing: Site specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev. 16:351-362.
  • Edgell, D.R. and Shub, D.A. (2001) Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites. Proc. Natl. Acad. Sci. USA 98:7898-7903.
  • Bonocora, R.P. and Shub, D.A. (2001) A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes. Mol. Microbiol. 39:1299-1306.
  • Edgell, D.R., Landthaler, M. and Shub, D.A. (2001) Intron homing. In Encyclopedia of Life Sciences , Nature Publishing Group, London.
  • Paquin, B. and Shub, D.A. (2001) Introns: Group I structure and function. In Encyclopedia of Life Sciences, Nature Publishing Group, London.
  • Shub, D.A. (2000). RNA splicing, bacterial. In Encyclopedia of Microbiology (J. Lederberg, ed.), vol. 4, pp.181 - 184, Academic Press, San Diego, CA
  • Edgell, D.R., Belfort, M. and Shub, D.A. (2000) Barriers to intron promiscuity in Bacteria. J. Bacteriol. 182:5281-5289.
  • Landthaler, M. and Shub, D.A. (1999) Unexpected abundance of self-splicing introns in bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proc. Natl. Acad. Sci. USA 96:7005-7010.
  • Paquin, B., Heinfling, A. and Shub, D.A. (1999) Sporadic Distribution of tRNA Arg (CCU) introns among alpha-purple bacteria: Evidence for horizontal transmission and transposition of a group I intron. J. Bacteriol. 181:1049-1053.
  • Paquin, B., Kathe, S.D., Nierzwicki-Bauer, S.A., and Shub, D.A. (1997) Origin and evolution of group I introns in cyanobacterial tRNA genes. J. Bacteriol. 179:6798-6806.[Click here for Intron Alignment]
  • Goodrich-Blair, H. and Shub, D.A. (1996) Beyond homing: Competition between intron endonucleases confers a selective advantage on flanking genetic markers. Cell 84:211-221.
  • Bechhofer, D., Hue, K.K., and Shub, D.A. (1994) A novel intron in the thymidylate synthase gene of Bacillus phage beta-22: Evidence for independent evolution of a gene, its group I intron,and the intron open reading frame. Proc. Natl. Acad. Sci. USA 91:11669-11673.
  • Biniszkiewicz, D., Cesnaviciene, E., and Shub, D.A. (1994) Self-splicing group I intron in a cyanobacterial initiator methionine tRNA: evidence for lateral transfer of introns in bacteria. EMBO J. 13:4629-4635.
  • Shub, D.A., Goodrich-Blair, H., and Eddy, S.R. (1994) Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. TIBS 19:402-404.
  • Goodrich-Blair, H. and Shub, D.A. (1994) The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames. Nucleic Acids Res. 22:3715-3721.
  • Young, P., Öhman M. , Xu, M.Q., Shub, D.A., and Sjöberg, B-M. (1994) Intron-containing T4 bacteriophage gene sunY encodes an anaerobic ribonucleotide reductase. J. Biol. Chem. 269:20229-20232.
  • Shub, D.A., Cotzee, T., Hall, D. and Belfort, M. (1994) The self-splicing introns of phage T4. In Molecular Biology of Bacteriophage T4, ed. J.D. Karam. ASM Press. pp. 186-192.
  • Shub, D.A. (1994) Bacterial altruism. Curr. Biol. 4:555-556.
  • Shub, D.A. and Goodrich-Blair, H. (1992) Protein introns: A new home for endonucleases. Cell 71:183-186.
  • Michel, F., Jaeger, L., Westhof, E., Kuras, R., Tihy, F., Xu, M.-Q. and Shub, D. A. (1992) Activation of the catalytic core of a group I intron by a remote 3' splice junction. Genes Dev. 6:1373-1385.
  • Reinhold-Hurek, B. and Shub, D.A. (1992) Self-splicing introns in tRNA genes of widely divergent bacteria. Nature 357:173-176.
  • Shub, D.A. (1991) The antiquity of group I introns. Curr. Opin. Genet. Dev. 1:463-469.
  • Zeeh, A. and Shub, D.A. (1991) The product of the split sunY gene of bacteriophage T4 is a processed protein. J. Bacteriol. 173:6980-6985.
  • Xu, M.-Q., Kathe, S.D., Goodrich-Blair, H., Nierzwicki-Bauer, S.A. and Shub, D.A. (1990) Bacterial origin of a chloroplast intron: Conserved self-splicing group I introns in cyanobacteria. Science 250:1566-1570.
  • Goodrich-Blair, H., Scarlato, V., Gott, J.M., Xu, M.-Q. and Shub, D.A. (1990) A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1. Cell 63:417-424.
  • Michel, F., Netter, P., Xu, M.-Q. and Shub, D.A. (1990) Mechanism of 3' splice site selection by the catalytic core of the sunY intron of bacteriophage T4: The role of a novel base pairing interaction in group I introns. Genes Dev. 4:777-888.

 

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