Virginia Walbot

Stanford University

I am interested in how genomic diversity is created and how biochemical pathways are assembled through gene duplication and promoter evolution. The specific areas of study are [1] regulation of MuDR transposons (Walbot 1991, 2000a), [2] deposition of anthocyanin pigment, the main visual marker for Mu activities (Marrs et al. 1995), and [3] developing genomics tools for maize gene tagging and sequencing using RescueMu, a genetically altered Mu element, and EST sequencing (Gai et al. 2000). Transposons are a major component of angiosperm genomes and the source of allelic diversity in maize (Walbot 1991); transposons contribute to the plasticity of plant responses and that transposons are subject to host and environmental regulation (Walbot 1996). The most active element system known is Mu/MuDR in maize. Mu elements are active only during terminal cell divisions of tissue development (Levy & Walbot 1990); in the soma, activation of Mutator results in element excision (ìcut & pasteî transposition), however, in pre-meiotic cells and in gametes, Mutator activation results in insertion without element excision (replicative transposition) (Walbot 1991; Walbot & Rudenko 2000). The ability to change transpositional mechanisms is a unique and exciting attribute of MuDR. We cloned and sequenced MuDR and defined the major transcripts of the convergently transcribed mudrA and mudrB genes (Hershberger et al. 1991, 1995). Using transgenic maize we established that one form of the transposase MURA (Benito & Walbot 1997) can catalyze somatic excision but not somatic insertion (Raizada & Walbot 2000), although MuDR programs both activities (Raizada, Nan & Walbot 2000). We discovered that MuDR-related elements in land races of maize (Gutierrez et al. 1998) and can now identify mudrA-like transposase genes in many dicots and in rice; the Mutator "superfamily" appears to be found in plants and prokaryotes only, suggesting horizontal transmission (Walbot & Rudenko 2000).

I manage the NSF funded Maize Gene Discovery project encompassing EST and genomic sequencing (Walbot 2000). Seeing the emerging large data sets (Walbot 1999) stimulates interest in attacking fundamental problems such as gene annotation. Alternative splicing of mudrA and mudrB transcripts results in multiple predicted proteins. This and other cases of retained introns and of Mu-induced alternative splicing outcomes (Luehrsen & Walbot 1990. 1994) has prompted us to investigate the "rules" for intron recognition in plants and to develop new tools for splice site prediction (Brendel et al. 1998). Our finding that Bz2, the last cytoplasmic step in maize anthocyanin biosynthesis, is catalyzed by a glutathione S-transferase (Marrs et al. 1995) also challenges understanding function based on phylogeny. In Petunia, a GST sharing only 11% identity with Bz2 is responsible for the same step in pigment biosynthesis (Alfenito et al. 1998). GSTs are a very large and divergent gene family (Edwards et al. 2000), important for the detoxification of many secondary metabolites and active oxygen species, yet the anthocyanin "specific" GSTs are regulated by the same transcription factors in all species examined (Alfenito et al. 1998; Lloyd et al. 1992). Is evolution of promoters more important than changes in the coding regions when new biochemical pathways are assembled?

Relationship to the Project:
I see the RCN as an ideal forum for exploring the distribution and types of transposons in plants. What would be the appropriate sampling method for determining the distribution of MuDR/Mu elements in other taxa? As transposons accumulate mutations more quickly than host genes, what new tools will be required to recognize them and other rapidly evolving sequences? Similarly, how are gene families and their promoters changing across broad taxonomic categories? Does expansion of the GSTs correspond to evolution of new secondary metabolites? How do polyploidy and genomic expansion fit with the changes in transposon and GST copy numbers? I see these and other issues as topics for fruitful discussions and future research initiatives.