Biology Faculty: David Shub

David Shub

Professor of Biological Sciences
Ph.D., Massachusettes Institute of Technology

Office BI324
Telephone (518) 442-4324
Lab Telephone (518) 442-4323
Fax (518) 442-4767
Email shub@albany.edu

Areas of Interest

  • Origin, evolution and function of self-splicing introns
  • Recombination between introns (exon shuffling)
  • Genetic analysis of intron structure and function




Research

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Origin, evolution and function of self-splicing introns

Until recently, it had been thought that RNA splicing occurs only in eukaryotes. We now know that genes encoding tRNAs in a variety of bacteria and mRNAs of viruses infecting E. coli and B. subtilis contain introns that are removed at the RNA level. The splicing event is autocatalytic, not requiring participation of proteins of other RNAs. These introns resemble the well-studied intron ribozyme of Tetrahymena, in both structure and splicing mechanism.

Our work is proceeding in two directions:
 
Origins and evolution

    Hypotheses have been advanced that (1) give catalytic RNA a central role in life's origin (the RNA world) and (2) propose that the structure of contemporary proteins is the result of extensive recombination between introns (exon shuffling). Absence of introns from eubacteria presented a serious drawback to these attractive ideas. Our analysis of the distribution and molecular evolution of bacterial introns will help to resolve whether introns were already present in the common ancestor of all living things.

Intron function

    If introns are indeed ancient, bacteria must have lost most of their introns. We assume that introns must provide a useful function in the rare cases where they have been retained. Through in vitro mutagenesis and DNA cloning, we are able to introduce intron-less copies of genes into bacteria. Insight into the role of intron splicing is obtained by observing differences in gene function and regulation. Genetic analysis of intron structure is used to determine the parameters required for activity of an RNA enzyme.

Publications

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  • Salman, V., Amann, R., Shub, D.A. and Schulz-Vogt, H.N. (2012). Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proceedings of the National Academy of Sciences ; published ahead of print February 27, 2012, doi:10.1073/pnas.1120192109
  • Bonocora, R.P., Zeng, Q., Abel, E.V. and Shub, D.A. (2011). A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette. Proc. Natl. Acad. Sci.USA. 108:16351-16356.
  • Zeng Q, Bonocora RP, Shub DA. (2009) A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages. Curr. Biol. 19: 218-222.
  • Bonocora RP, Shub DA. (2009) A likely pathway for formation of mobile group I introns. Curr. Biol. 19: 223-228.
  • 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. 26:2432-2442.
  • 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.