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use CXGN::Page;

my $page = CXGN::Page->new("SGN Featured Lab: The Tobacco Research Group in the Timko Lab", "Adri");

$page->header("The Tobacco Research Group in the Timko Lab", "The Tobacco Research Group in the Timko Lab");

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<p>The Tobacco Research Group in the Timko Laboratory is interested in understanding the enzymology of major and minor leaf alkaloid biosynthesis in cultivated tobacco and the genes and signal transduction processes that control the formation and accumulation of leaf alkaloids during normal growth and development and in response to various biotic and abiotic stresses.</p>

<center>
<img src="/static_content/community/feature/200806-group.png" width="70%" />

<p>Left to right: Jim Roberts, Shengcheng Han, Michael Timko, Hongbo Zhang, Marta Bokowiec, <br />
John Finer, Paul Rushton, Jeff Chen. (Missing from photograph is Tom Laudeman.)</p>
</center>

<p>Cultivated tobacco (<em>Nicotiana tabacum</em> L.) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants that includes eggplant, pepper, petunia, potato, and tomato. <em>N. tabacum</em> is an amphiploid species (2n=48) resulting from an interspecific cross between two wild forms, <em>N. sylvestris</em> (2n=24) and <em>N. tomentosiformis</em> (2n=24). Domesticated tobacco has been cultivated for several thousand years and was widely used by the indigenous peoples in the Americas for medicinal and ceremonial purposes.</p>

<p>Both the wild and domesticated forms of tobacco accumulate a wide variety of alkaloids, the content and composition of which vary among species. The most abundant of the alkaloids produced in wild and cultivated tobacco (<em>Nicotiana</em>) are nicotine, nornicotine, anabasine, and anatabine. In most commercial tobacco varieties, nicotine represents 90-95% of the total alkaloid content of the leaf, with the remainder of the alkaloid pool accounted for by minor alkaloids present in varied amounts depending on cultivar.</p>

<p>We now understand that the biosynthesis of nicotine and its derivatives is controlled by a variety of factors. Among the major endogenous factors, changes in levels and/or ratios of various phytohormones (e.g., auxin, ethylene) as a consequence of plant development stimulate nicotine formation in the roots and its translocation to the leaves. Removal of the flowering stalk during commercial tobacco growing is well know to induce alkaloid formation and nicotine accumulation, either through a wound response or via auxin derepression.  Biotic stresses (such as insect herbivory) have also been shown to stimulate the synthesis and accumulation of nicotine and its derivatives. This process is tied into a jasmonic acid (JA) response cascade.</p>

<p>Using an integrated approach that includes biochemical analysis, genome sequencing and bioinformatics, reverse genetics, and microarray-based gene expression profiling we are attempting to identify the genes that encode the enzymatic machinery of alkaloid formation and the transcription factors (TFs) and basic signal transduction components that control gene expression in the major and minor alkaloid biosynthesis pathways in tobacco. Our studies use wild type and transformed BY-2 tobacco suspension cultures and whole plants, in combination with various chemical and phytohormonal treatments, to discern regulatory elements/motifs in the promoters of genes encoding key enzymes in nicotine and minor alkaloid formation. These transgenic studies are complemented by various in vivo and in vitro approaches (e.g., yeast 1- and 2-hybrid analyses, gel mobility shift assays) to define the specific transcription factors (TFs) and TF complexes that bind these elements to promote or repress gene expression.</p>

<p>Among the current focuses of the laboratory at present is understanding the role of jasmonic acid (JA) and JA signaling in the regulation of alkaloid formation during development and in response to wounding and resistance to herbivore attack. To this end we are defining the TFs and promoter elements that mediate JA-responsiveness in several key alkaloid biosynthesis genes including putrescine N-methyltransferase, quinolinic acid phosphoribosyltransferase, and nicotine demethylase. To accomplish this we are using BY-2 cell cultures as a model in combination with targeted gene alteration and gene expression profiling with Nimblegen microarrays.</p>

<p>Compared with other cultivated Solanaceous plants <em>N. tabacum</em> has a very large genome size with approximately 4.5 billion base pairs (~1.5 times the size of the human genome). The <a href="http://www.tobaccogenome.org/">Tobacco Genome Initiative (TGI)</a> has generated over one million gene-space sequence reads (GSRs) from methylation-filtered (MF) tobacco genomic DNA libraries prepared from “Hicks Broadleaf”, a highly inbred and fairly homozygous cultivar. The availability of these GSRs facilitates genome wide-analysis, large-scale functional genomics and gene discovery.</p>

<p>The transcriptional regulation of gene expression is a major control point in many biological processes and plant genomes devote approximately 7% of their coding sequence to transcription factors (TFs). Headed up by Paul Rushton, we have performed an <em>in silico</em> analysis of 1.15 million gene space sequence reads from the tobacco nuclear genome and report the detailed analysis of over 2,500 tobacco transcription factors (TFs). Our studies show that the tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes. Therefore, it appears that evolution of the Solanaceae was not associated with wholesale gain or loss of TF families.</p>

<p>To facilitate subsequent comparison and analysis, we have constructed an expandable knowledgebase called <a href="http://compsysbio.achs.virginia.edu/tobfac/">TOBFAC: The Database of Tobacco Transcription Factors</a>. TOBFAC provides access to the currently available TF sequences from tobacco (the largest data set from any member of the Solanaceae, including the first reported information on over 40 tobacco TF families), comparative phylogenetic analysis, as well as available EST data, published reports, sequences of tobacco TFs and a large quantity of other data concerning TFs in tobacco.</p>

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<h4>Selected Publications</h4>

<p>Rushton PJ, Bokowiec MT, Han S, Zhang H, Brannock JF, Chen X, Laudeman TW, and
Timko MP (2008) Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae. Plant Physiology 147: 280-295.</p>

<p>Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, and Timko MP (2008) TOBFAC: the database of tobacco transcription factors. BMC Bioinformatics 9:53 doi:10.1186/1471-2105-9-53.</p>

<p>Xu B and Timko MP (2004) Methyl jasmonate induced expression of the tobacco putrescine N-methyltransferase genes requires both G-Box and GCC-motif elements. Plant Mol. Biol. 55: 743-761.</p>

<p>Xu B, Sheehan M, and Timko MP (2004) Differential induction of ornithine decarboxylase (ODC) gene family members in transgenic tobacco (Nicotiana tabacum L. cv Bright Yellow 2) cell suspensions by methyl-jasmonate treatment. Plant Growth Regulation 44: 101-116.</p>

<p>Ren N and Timko MP (2001) AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species. Genome 44: 559-571.</p>

<p>Wang J, Sheehan M, Brookman H, and Timko MP (2000) Characterization of cDNAs differentially expressed in the roots of tobacco (Nicotiana tabacum cv Burley 21) during the early stages of alkaloid biosynthesis. Plant Sci. 158: 19-32.</p>

<p>Wang J, Sheehan M, and Timko MP (2000) Differential expression of two members of the nuclear gene family encoding arginine decarboxylase (ADC) in tobacco (Nicotiana tabacum L.)  J. Plant Biochem. Biotech 9: 57-65.</p>


<h4>Contact Information</h4>

Michael P. Timko<br />
Department of Biology<br />
University of Virginia<br />
Charlottesville, Virginia 22903<br />
Tel: 434-982-5817 (Office) or -5779 (Lab)<br />
Fax:  434-982-5626<br />
e-mail: mpt9g\@virginia.edu<br />
URL: <a href="http://faculty.virginia.edu/timko/home.htm">http://faculty.virginia.edu/timko/home.htm</a>,<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<a href="http://faculty.virginia.edu/timko/tobacco_genomics.htm">http://faculty.virginia.edu/timko/tobacco_genomics.htm</a>

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