Publications

Publications in 2007

Publications in 2005 - 2006

Kirst, M., R. Caldo, P. Casati, G. Tanimoto, V. Walbot, R. P. Wise, and E. S. Buckler. 2006. Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnology Journal 4:

Ma, J., D .J. Morrow, J. Fernandes, V. Walbot. 2006. Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biology 7:R22 doi:10.1186/gb-2006-7-3-r22

Casati, P., A. E. Stapleton, J. E. Blum, and V. Walbot. 2006. Genome-wide analysis of high altitude maize and gene knockdown implicates chromatin remodeling proteins in response to UV-B. Plant Journal 46: 613-627.

Rudenko, G. N., G.-I. Nan, and V. Walbot. 2005. Progress and perspectives in maize gene discovery. Maydica 50: 393-404. Special 50th anniversary volume, invited paper.

Rudenko, G. N., A. Ono, and V. Walbot. 2005. An early excision variant of the MuDR/Mu transposon family is not associated with a local duplication of the bz1::Mu1 allele. Maydica 50, in press. Invited paper for a memorial volume.

Walbot, V. 2005. OBPC Symposium: Maize 2004 & Beyond - Regulation of the MuDR/Mu transposable elements of maize and their practical uses. In vitro Cell. Dev. Biol.-Plant 41: 374-377.

Casati, P., X. Zhang, A. L. Burlingame, and V. Walbot. 2005. Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol. Cell. Proteomics 4: 1673-1685.

Casati, P. and V. Walbot. 2005. Differential accumulation of maysin and rhamnosylisorientin in leaves of high altitude landraces of maize after UV-B exposure. Plant Cell Environment 28: 788-799. doi:10.1111/j.1365-3040.2005.01329.x

Publications in 2003 - 2004

Casati, P. and V. Walbot. 2004. Crosslinking of ribosomal proteins to RNA in vivo after UV-B irradiation of maize leaves. Plant Physiology 136: 3319-3332.

Fernandes, J., Q. F. Dong, B. Schneider, D. J. Morrow, G. L. Nan, V. Brendel, and V. Walbot. 2004. Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biology 5: doi:10.1186/gb-2004-5-10-r82

Walbot, V. 2004. Genomic, chromosomal and allelic assessment of the amazing diversity of maize. Genome Biology 5:328 doi:10.1186/gb-2004-5-6-328

Blum, J. E., P. Casati, V. Walbot, and A. E. Stapleton. 2004. Split-plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population. Plant, Cell and Environment 27: 1374-1386.

Goodman, C. D., P. Casati, and V. Walbot. 2004. A multidrug-resistance associated protein involved in anthocyanin transport In Zea mays. Plant Cell 16: 1812-1826.

Casati, P. and V. Walbot. 2004. Rapid molecular responses of maize to UV-B: gene expression profiling in irradiated and shielded tissues. In press, Genome Biology.

Pairoba, C. F. and V. Walbot. 2004. Post-transcriptional regulation of expression of the maize Bronze2 gene of Zea mays L. Plant Molecular Biology 53: 75-86.

Lunde, C. F., D. R. Morrow, L. M. Roy and V. Walbot. 2003. Progress in Maize Gene Discovery: a project update. Functional Integrative Genomics 3: 25-32. On-line version: October 1, 2002:, DOI 10.1007/s10142-002-0078-y.

Larsen, E., M. R. Alfenito, W. R. Briggs and V. Walbot. 2003. A carnation anthocyanin mutant is complemented by Bz2, a maize glutathione S-transferase. Plant Cell Reports 21: 900 - 904.

Kim, S.-H. and V. Walbot. 2003. Structural and functional analysis of antisense MuDR transcripts: insensitivity of maize Mutator transposon activities to endogenous and transgene-encoded antisense RNA. Plant Cell 15: 2430-2447.

Casati, P. and V. Walbot. 2003. Gene expression profiling in response to ultraviolet radiation in Zea mays genotypes with varying amounts of flavonoids. Plant Physiology 132: 1739-1754.

Walbot, V. and M. M. Evans. 2003. Unique features of the plant life cycle and their consequences. Nature Reviews Genetics 4: 369 -379.

Dong, Q. F., L. Roy, M. Freeling, V. Walbot and V. Brendel. 2003. ZmDB, an integrated database for maize genome research. Nucl. Acids Res. 31: 244-247.

Rudenko, G. N., A. Ono, and V. Walbot. 2003. Initiation of silencing of maize MuDR/Mu transposable elements. Plant Journal 33: 1013-1025.

Publications in 2000 - 2002

Cho, Y., J. Fernandes, S.-H. Kim, and V. Walbot. 2002. Gene expression profile comparisons distinguish thirteen organs of maize. Genome Biology 3:research0045.1-0045.16. view online

Ono, A.. S.-H. Kim, and V. Walbot. 2002. Subcellular localization of MURA and MURB proteins encoded by the maize MuDR transposon. Plant Molecular Biology 50: 599-611.

Brendel, V., S. Kurtz, and V. Walbot. 2002. Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biology 3: 1005.1-1005.6

Fernandes, J., V. Brendel, X. Gai, S. Lal, V. L. Chandler, R. Elumalai, D. W. Galbraith, E. Pierson, and V. Walbot. 2002. Comparison of RNA expression profiles based on maize EST frequency analysis and microarray hybridization. Plant Physiology 128: 896-910.

Bennetzen, J., E. Buckler, V. Chandler, J. Doebley, J. Dorweiler, B. Gaut, M. Freeling, S. Hake, E. Kellogg, R. S. Poethig, V. Walbot, and S. Wessler. 2000. Genetic evidence and the origin of maize. Latin American Antiquity 12: 84-86.

Raizada, M. N., G. L. Nan and V. Walbot. 2001. Somatic and germinal mobility of the RescueMu transposon in transgenic maize. Plant Cell 13: 1587-1608.

Cho, Y. and V. Walbot. 2001. Computational methods for gene annotation: the Arabidopsis genome. Current Opinion in Biotechnology12: 126-130.

Walbot, V. 2001. Imprinting of R-r, paramutation of B-I and Pl, and epigenetic silencing of MuDR/Mu transposons in Zea mays L. are co-ordinately affected by inbred background. Genetical Research 77: 219-226.

Walbot, V. and G. N. Rudenko. 2002. MuDR/Mu transposons of maize. In: Mobile DNA II, eds. N. L. Craig, R, Craigie, M. Gellert, A. Lambowitz. Amer. Soc. Microbiology, Washington, D. C. pp. 533-564.

Rudenko, G. N. and V. Walbot. 2001. Expression and post-transcriptional regulation of maize transposable element MuDR and its derivatives. Plant Cell 13:553-570.

Walbot, V. 2001. Genomics: New tools to analyze genetic and biochemical diversity. Recent Adv. Phytochemistry, Vol. 35, eds. John T. Romeo, James A. Saunders, and Benjamin F. Matthews. New York : Elsevier Science Ltd. pp. 1-14.

Mueller, L. A. and V. Walbot. 2001. Models for anthocyanin sequestration. Recent Adv. Phytochemistry, Vol. 35, eds. John T. Romeo, James A. Saunders, and Benjamin F. Matthews. New York : Elsevier Science Ltd. pp. 297-317.

Walbot, V. 2001. Impact of transposons on the maize genome. Ch. 3 (provisional) In: Cronk, Q.C.B., Bateman, R. and Hawkins, J.A. (eds) Developmental Genetics and Plant Evolution. London: Taylor and Francis. In press.

Raizada, M. N., M.-I. Benito and V. Walbot. 2001. The MuDR transposon terminal inverted repeat contains a complex plant promoter directing distinct somatic and germinal programs. Plant J 25: 1-15.

Raizada, M. N., K. V. Brewer and V. Walbot . 2001. A maize MuDR transposon promoter shows limited autoregulation. Molecular Genet. Genomics 265: 82-94.

Walbot, V. 2000. Green chapter in the book of life. Nature 408: 794-795.

Mueller, L. A., C. D. Goodman, R. A. Silady and V. Walbot. 2000. AN9, a Petunia glutathione S-transferase required for anthocyanin sequestration, is a flavonoid-binding protein. Plant Physiology 123: 1561-1570.

Edwards, R., Dixon, D. P. and V. Walbot. 2000. Plant glutathione S-transferases: multifunctional enzymes aiding survival in a hostile world. Trends in Plant Science 5: 193-198.

Raizada, M. and V. Walbot. 2000. The late developmental pattern of Mu transposon excision is conferred by a CaMV 35S-driven MURAcDNA in transgenic maize. Plant Cell 12: 5-22

Walbot, V. 2000. Saturation mutagenesis using maize transposons. Current Opinion in Plant Biology 3: 103-107. Edwards, R., Dixon, D. P. and V. Walbot. 2000. Plant glutathione S-transferases: multifunctional enzymes aiding survival in a hostile world. Submitted, Trends in Plant Science.

Walbot, V. 2000. Saturation mutagenesis using maize transposons. Submitted to Current Opinion in Plant Biology.

Raizada, M. and V. Walbot. 2000. The late developmental pattern of Mu transposon excision is conferred by a CaMV 35S-driven MURA cDNA in transgenic maize. Plant Cell January issue, pp. 1-17.

Gai, X., S. Lal, L. Xing, V. Brendel and V. Walbot. 2000. Gene discovery using the maize genome database ZmDB. Nucleic Acids Research 28 http://www3.oup.co.uk/nar/Volume_28/Issue_01/gkd073_gml.abs.html

Publications in 1997 -1999

Walbot, V., L. Mueller, R. A. Silady, and C. D. Goodman. 1999. Do glutathione S-transferases acts as enzymes or as carrier proteins for their natural substrates? In: Sulfur metabolism in higher plants, molecular, biochemical and physiological aspects. Brunold, C., Rennenberg, H., Davidian, J., Stulen, I. and De Kok, L. eds., Paul Haupt, Bern. In press.

Walbot, V. 1998. Solar UV-B irradiation of maize pollen can reactivate silent Mutator transposable elements. In press, Nature (title will likely be changed by the journal).

Walbot, V. and A. Stapleton. 1998. Reactivation potential of epigenetically inactive Mu transposable elements of Zea mays L. decreases in successive generations. Maydica 43: 183-193. This article establishes that inactive Mutator lines become progressively refractory to activation by the introduction of transcriptionally active MuDR elements; it provides control data for the Nature paper on UV-B reactivation.

Alfenito, M. R., E. Souer, R. Buell, R. Koes, J. Mol and V. Walbot. 1998. Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases. Plant Cell 10: 1135-1149 (including cover photo).

Brendel, V., J. C. Carle-Urioste, and V. Walbot. 1998b. Intron recognition in plants. In: J. Bailey-Serres & D. R. Gallie, Eds. A Look Beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants, pp.20-28. Amer. Soc. Plant Physiol., Rockville, MD.

Brendel, V., J. Kleffe, J. C. Carle-Urioste, and V. Walbot. 1998. Prediction of splice sites in plant pre-mRNA from sequence properties. J. Mol. Biol. 276: 85-104.

Ko, C. H., V. Brendel, R. D. Taylor and V. Walbot. 1998. U-richness is a defining feature of plant introns andmay function as an intron recognition signal in maize. Plant Mol. Biol. 36: 573-583.

Gutiérrez-Nava, M., C. Warren and V. Walbot. 1998. Transcriptionally active MuDR, the regulatory element of the Mutator transposable element family of Zea mays, is present in some accessions of the Mexican land race Zapalote chico. Genetics 149: 329-346.

Benito, M.-I. and V. Walbot. 1997. Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein. Mol. Cellular Biology 17: 5165-5175.

Stapleton, A. E., C. S. Thornber and V. Walbot. 1997. UV-B component of sunlight causes measurable damage in field-grown maize (Zea mays L.): Developmental and cellular heterogeneity of damage and repair. Plant, Cell & Environment 20: 279-290.

Carle-Urioste, J., V. Brendel and V. Walbot. 1997. A combinatorial role for exon, intron and splice site sequences in splicing in maize. Plant J. 11: 1253-1263. We propose a combinatorial "co-operation" between exon motifs, intron composition and the splice sites in defining maize introns. By analyzing a database of maize introns for common features, we propose a method for identifying introns in new sequence based on the bias for GC in exons and U-bias in introns, plus splice site quality.

Stapleton, A. E., C. S. Thornber and V. Walbot. 1997. UV-induced damage and repair in maize (Zea mays L.): Developmetnal, cellular and subcellular characterization. We report the heterogeneity of damage to epidermal vs. interior cells and demonstrate that both zones repair UV-induced CPD and 6/4 photoproducts. We also found that dimers are removed by photolyase(s) from nuclear, plastid and mitochondrial genes. In contrast the Britt lab recently reported that organellar damage is not repaired in Arabidopsis seedling roots. Plant, Cell & Environment 20: 279-290.

Marrs, K. A. and V. Walbot. 1997. Expression and RNA splicing of the maize glutathione S-transferase Bronze2 is regulated by cadmium and other stresses. Plant Physiology 113: 93-102.

Joanin, P., R. J. Hershberger, M.-I. Benito and V. Walbot. 1997. Sense and antisense transcripts of the maize MuDR regulatory transposon localized by in situ hybridization. Plant Molecular Biology 33: 23-36.

Landry, L. G., A. E. Stapleton, J. Lim, P. Hoffmann, J. B. Hays, V. Walbot and R. L. Last. 1997. Photoreactivation repair of ultraviolet radiation-induced DNA damage is essential for Arabidopsis survival. Knocking out the gene that encodes the phytolyase that reverses cyclobutane pyrimidine dimers is lethal. Proc. Natl. Acad. Sci. USA. 94: 328-332.

Li, Z.-S., M. Alfenito, P. A. Rea, V. Walbot and R. A. Dixon. 1997. Vacuolar uptake of glutathionated medicarpin by the glutathione conjugate pump. Phytochemistry 45: 689-693.

Publications in 1995 & 1996

Bodeau, J. P. and V. Walbot. 1996. Structure and regulation of the maize Bronze2 promoter. Plant Mol. Biol. 32: 599-609 This article reports many details of Bz2 promoter organization and confirms early findings of multiple initiation sites; at least in transient assays in BMS protoplasts, the Bz2 promoter is completely dependent on the R and C1 proteins.

Walbot, V. 1996. Sources and consequences of phenotypic and genotypic plasticity in flowering plants. Trends in Plant Science. 1: 27-32. A review of the plant life cycle and means to generate genomic diversity and phenotypic plastidicity; the article includes a discussion of imprinting and regularity of embryo development.

Hershberger, R. J., M.-I. Benito, K. J. Hardeman, C. Warren, V. L. Chandler and V. Walbot. 1995. Convergent transcripts, antisense RNA, and splicing failure in the maize Mutator element MuDR. Genetics 140: 1087-1098. Article that defines the transcripts of MuDR, the master element of Mutator transposons. Article also provides evidence that internally dd MuDR elements are transcriptionally active; northern blot surveys of transcripts in various tissues indicate that MURA and MURB transcripts are abundant and ubiquitous. "splicing failure" seems to play a big role, particularly in MURB transcripts which often retain two in-frame introns (120 bases and 72 bases); MURA has two start sites and there is splicing failure in the third introns so that 4 distinct mRNAs exist for this gene as well.

Marrs, K. A., M. R. Alfenito, A. M. Lloyd and V. Walbot. 1995. A glutathione-S-transferase involved in vacuolar transfer encoded by the maize gene Bronze-2. Nature 375: 397-400. Finally, we know what BZ2 does: it tags cytoplasmic cyanidin 3-glucoside with glutathione, and this conjugate is recognized by an ABC transporter in the tonoplast membrane. The ABC transporter uses ATP directly and is not impaired by drugs that discharge the proton gradient; this class of pumps is inhibited by vandate.

Andre, C. P. and V. Walbot. 1995. Pulsed-field gel mapping of maize mitochondrial chromosomes. Mol. Gen. Genetics 247: 255-265. Circle after circle after circle can explain the genome.

Nordborg, M. and V. Walbot. 1995. Estimating allelic diversity generated by excision of different transposons types. Theoretical Appl. Genetics 90: 771-775. We provide an algorithm that will predict the number and sequence of excision alleleson; you supply the range of length of deletion or insertion.

Bodeau, J. P. and V. Walbot. 1995. Genetic control of anthocyanin accumulation in embryogenic maize callus. Maydica 40: 77-83.Description of the tissue culture anthocyanin phenotypes of a large number of A188 embryogenic lines in specific regulatory gene backgrounds.Seed have been supplied to the Co-op for these lines. Special issue dedicated to E. H. Coe.

Publications in 1994

Benito, M.-I. and V. Walbot. 1994. Promoter elements active in maize cells are located within the terminal inverted repeat sequences of MuDR. Maydica 39: 255-264. The TIRs are weak but functional in BMS protoplasts in transient assays; promoter activity is not influenced by co-expression of the MURB protein. Special dedicated to Donald Robertson.

Carle-Urioste, J. C., C. Ko, M.-I. Benito and V. Walbot. 1994. Splicing success and splicing failure vector pairs for analysis of pre-mRNA fate. Plant Mol. Biol. 26: 1785-1795. Establishing conditional splicing assays with luciferase vectors; one vector type (pSuccess) can only encode luciferase if splicing occurs while the partner pFail vector encodes luciferase from unspliced mRNA; in this way changes in individual nucleotides can be checked in a positive and a negative assay.

Galway, M. E., J. D. Masucci, A. M. Lloyd, V. Walbot, R. W. Davis and J. W. Schiefelbein. 1994. The TTG gene is required to specify epidermal cell fate and cell patterning in the Arabidopsis root. Developmental Biology 166: 740-754. We really wish we had TTG cloned, but here is some more information about what the maize R regulatory gene of the anthocyanin pathway can do. In ttg backgrounds, many additional ranks of root epidermal cells make root hairs; this phenotype is suppressed by R. Both R and TTG have "reciprocal" effects in the root and shoot.

Lloyd, A. M., M. Schena, V. Walbot and R. W. Davis. 1994. Epidermal cell fate determination in Arabidopsis: patterns defined by a steroid-inducible regulator. Science 266: 436-439. A new tool for monitoring the impact of R by allowing expression of a non-functional protein; the time and place of "activation" are determined by when and where the investigator adds the appropriate steriod hormone; a good tool for defining "developmental windows."

Eisen, J. A., M.-I. Benito and V. Walbot. 1994. Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. Nucleic Acids Research 13: 2634-2636. MURA gene resembles a diverse set of bacterial insertion elements, not previously recognized as a common group.

Luehrsen, K. R. and V. Walbot. 1994. AUG context for translational initiation in maize cells. Plant Cell Research 13: 454-458. Maize shows relaxed requirements for the AUG context and can use multiple AUGs in a series. Other work demonstrates internal initiation by making compound mRNAs. Clearly the dogma that only the first AUG is meaningful if in a good context is not so applicable to plants.

Walbot, V., M-I. Benito, J. Bodeau and J. Nash. 1994. Abscisic acid induces pink pigmentation in maize aleurone tissue in the absence of Bronze-2. Maydica 39: 19-28. Funny to read the speculation about the role of BZ2, before we had a clue. Paper does outline a neat trick for inducing anthocyanin in developing kernels by painting ABA onto developing ears. Special issue dedicated to M. G. Neuffer.

Luehrsen, K. R. and V. Walbot. 1994. Intron creation and polyadenylation in maize are directed by AU-rich RNA. Genes & Dev. 8: 1117-1130. A key paper in understanding the rules for intron recognition; main protocol is intron creation by inserting internal segments of introns into cDNAs. Intron U-content and a minimum length of about 100 bases seem sufficient; plant finds adequate splice sites near the borders of the insertion.

Christie, P. J., M. R. Alfenito and V. Walbot. 1994. Impact of low-temperature stress on general phenylpropanoid and anthocyanin pathways: Enhancement of transcript abundance and anthocyanin pigmentation in maize (B73N) seedlings. Planta 194: 541-549. Many labs have identified cold-induced genes of unknown function -- we've concentrated on analyzing regulation of anthocyanin synthesis and find that this pathway is activated by cold treatment. It's not just another way to get pretty purple plants. Could the extra pigment be important in heat gain in a cool climate? Ecologists and systematics experts report clines of non-pigmented plants in warm valleys with progressively darker plants with increased altitude. Corn from the Andes is very dark purple.

Stapleton, A. and V. Walbot. 1994. Flavonoids protect maize DNA from UV damage. Plant Physiology 105: 881-889. Demonstration that flavoniod-less and anthocyanin-less plants suffer more DNA damage; we used antibodies to cyclobutane pyrimindine dimers and to 6,4photoproduct dimers to monitor damage levels.

Luehrsen, K. R. and V. Walbot. 1994. Addition of A- and U-rich sequence increases the splicing efficiency of a deleted form of maize intron. Plant Molecular Biology 24: 449-463. First step in the intron improvement program.

Luehrsen, K. R., S. Taha and V. Walbot. 1994. Nuclear pre-mRNA processing in higher plants. Prog. Nucl. Acid Biochem. Mol. Biol. 47: 149-193. Useful review, including a section on maize transposon insertions.