UW Genome Sciences

Research:

In the early 1970s, Dr. Hall's group began work on the yeast Saccharomyces cerevisiae. They found three RNA polymerases in yeast with properties closely paralleling those of the RNA polymerases of mammalian cell nuclei. Subsequent research in the Hall lab and in many others has made yeast the system of choice for genetic exploration of eukaryotic RNA polymerase function. To facilitate molecular genetic studies in yeast, Dr. Hall's work first concentrated on developing methods to clone and characterize yeast genes of interest for the study of transcription. Those isolated include the CYC1 and mating-type loci, as well as several yeast suppresser tRNA genes. The initial work on these genes focused upon the promoter and terminator elements required for transcription by yeast RNA polymerases II and III.

Recent research in Dr. Hall's laboratory combines directed mutagenesis and in vivo screening for altered transcription with subsequent biochemical study of mutant polymerases to identify the location of specific functions within the yeast RNA polymerase III molecule. To a remarkable degree, the detailed positions of various catalytic motifs in this eukaryotic RNA polymerase mirror those recently determined for the E. coli enzyme (see Landick and Roberts, The Shrewd Grasp of RNA Polymerase. Science 273:202-203). A major current objective is to identify regions of the Pol III catalytic subunit that, when mutated, decrease the fidelity of transcription.

Since 1994, Dr. Hall has held a half-time position in the Botany Department, as well as in Genetics. There he is involved in several molecular evolution projects, using the genes encoding major subunits of RNA Polymerase II to track the evolutionary history of the nuclear genome. Recently, there has been wide acceptance of the proposal that the genesis and subsequent divergence of photosynthetic eukaryotes involved one primary endosymbiosis, leading from a single cyanobacterium to both red and green plastids. This theory has fueled the argument that present-day rhodophyte algae and green plants both descended from this hypothetical ancestor. Our studies of nuclear gene evolution suggest that the reasoning behind the unitary endosymbiosis concept is seriously flawed. While all available molecular indices place green plants within the "crown" group of higher eukaryotes, comparison with the nuclear genes of rhodophytes indicate the latter group diverged earlier, before the common ancestor of plants, animals and fungi. Other questions of botanical interest are also being pursued using molecular genetics. These include:

The evolutionary origin of seed plants, and the population history of the west coast rhododendron species R. macrophyllum, as inferred from current population structure measured at the DNA level.

Selected Publications:

Denton, A.L., McConaughy, B.L., and Hall, B.D. 1998. Usefulness of RNA Polymerase II Coding Sequences for Estimation of Green Plant Phylogeny. Mol. Biol. Evol 15:1082-1085.

Stiller, J.W., Duffield, E.C.S., and Hall, B.D. 1998. Amitochondriate amoebae and the evolution of DNA-dependent RNA polymerase II. Proc. Natl. Acad. Sci. USA 95:11769-11774.

Stiller, J. W. and Hall, B.D. (1998) Sequences of the Largest Subunit of RNA Polymerase II From Two Red Algae and Their Implications for Rhodophyte Evolution. J. Phycol. 34: 857-864.

Stiller, J.W. and Hall, B.D.(1999). Long-Branch Attraction and the rDNA Model of Early Eukaryotic Evolution. Mol.Biol.Evol. 16:1270-1279.

Liu, Y., Whelen, S., and Hall, B.D. (1999) Phylogenetic Relationships Among Ascomycetes: Evidence From an RNA Polymerase II subunit. Mol.Biol.Evol. 16(12):1799-1808.