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Utpal Nath
Associate Professor
Ph. D. (NCBS, Bangalore, India)
Phone: +91 80 22932414
E.mail: utpal@mcbl.iisc.ernet.in
URL : http://mcbl.iisc.ernet.in/Welcome%20to%20MCBL/Faculty/Nath/lab%20webpage/Front%20page.htm

We are studying plant growth and development using various molecular genetic techniques and Arabidopsis & Antirrhinum as model systems.
Control of organ morphogenesis in plants : The molecular basis of early events in plant development such as patterning the apical meristem and specifying organ identity have been studied in great detail.  Yet how this regional information is translated into the mature organ of a particular shape and size is poorly understood.  For example, it is not clear how various cell types differentiate in a coordinated manner to shape up the final structure of a leaf or a petal.  Our laboratory is interested in studying the genetic basis of organ growth and development in plants.

TCP4 mutants :  It has been shown that the CINCINNATA (CIN) gene, which codes for a transcription factor belonging to the TCP family, controls leaf shape and size in Antirrhinum (Nath et al., 2003; Crawford et al., 2004) by repressing cell proliferation.  However, it is not clear how CIN controls cell division in a patterned manner.  To address this problem, we are analysing the function of CIN orthologue in Arabidopsis, TCP4.
We have studied the expression pattern of TCP4 in developing leaves of Arabidopsis by reporter gene analysis.  TCP4 message is expressed throughout young leaves, and progressively gets restricted towards the base as the leaves develop.  This suggests that TCP4 controls leaf morphogenesis in the similar manner as CIN does in Antirrhinum.  To study TCP4 function in more detail, we have isolated several TCP4 alleles.  Analysis of these alleles established that TCP4 has dual function in leaf growth and embryo development.
TCP4 targets :  TCP4 codes for a DNA-binding transcription factor.  It is possible that TCP4 activates target gene(s) that is responsible for the repression of cell division in proliferating organ.  To identify the direct targets of TCP4, we have determined consensus-binding site of TCP4 protein using random binding site selection (RBSS) assay.  Using a combination of PCR and electrophoretic mobility shift assay, we have determined that TCP4 protein binds to a consensus sequence of GTGGTCCC.
To identify the target genes that are regulated by TCP4 in vivo, we have generated a transgenic line where TCP4 function can be activated upon addition of a chemical called dexamethasone.  When we induce TCP4 all over the plant at the seedling stage, we find that the leaf growth gets reduced drastically due to reduced cell number indicating that TCP4 is sufficient to repress cell division in plants.  We are now using this plant to identify direct targets of the TCP4.


Control of flowering time in Arabidopsis :  To maximise its reproductive success, plants must flower when adequate number of leaves are made to supply food to the flowers, and environmental factors are most conducive.  Hence, flowering time is tightly regulated by many genes; some of them are independent of environment whereas others are influenced by the environmental factors such as light, temperature etc.  We have isolated mutants for two homologous genes in Arabidopsis that are required to promote flowering.  In the single mutants of these genes, flowering is delayed to a moderate extent, whereas the double mutants flower very late.  This delay in flowering is further enhanced when plants are grown on short day length condition, indicating that these genes interact with the light-sensing pathway in the plant.  Reporter gene analysis and RNA in situ hybridization data shows that these genes are expressed in the vascular tissue.  Taken together, this demonstrates that these two Zn-binding transcription factors are present in the xylem and phloem but controls the transition of the shoot meristem to flowering, presumably through long distance signalling.  Several genes have been isolated by other groups that control flowering time through long distance signalling and we are now establishing how our genes interact with these known factors.
Screening for novel leaf mutants :  In spite of isolation and characterization of several genes involved in leaf morphogenesis, the genetic pathways involved in such process remain unclear.  To isolate new genes involved in controlling leaf shape and size in Arabidopsis, we are isolating novel leaf mutants by screening a large number of EMS-mutagenized M2 seeds for mutant lines with altered leaf morphology.  We have already isolated several plants with deformed leaf structure.  Two of the mutants are of particular interest to us.  The first one is parisal, a mutant where leaves buckle up to form a boat-shaped structure (hence the name parisal, means “coracle” in a local language here).  Apart from this, all the organs in this mutant such as leaves, sepals, petals, fruit and seeds are wider and shorter compared to the wild type.  This indicates that the gene PARISAL is required for proper polar growth of axillary organs.  We have mapped this mutation within 1 MB on the left arm of the 3rd chromosome.  We are currently trying to develop a high-resolution map of this mutant in order to clone the gene.  The other mutant that we are working on is called tooth, because the leaf margin in this mutant is serrated, as opposed to smooth in wild type.  We have mapped this mutant on 2nd chromosome within 7 cM and the locus does not appear to be allelic to any known mutant with serrated margin.  We are currently generating a high resolution map of this mutant and eventually clone the gene.

Selected Publications

Schommer, C., Palatnik, J. F., Aggarwal, P., Chételat, A., Cubas, P., Farmer, E. E., Nath, U. and Weigel, D. (2008). Control of Jasmonate Biosynthesis and Senescence by miR319 Targets. PLoS Biology 6(9):1-11.

Nath, U., Dixon, R. A., Coen, E. S., & Lawson, D. M. (2006). Crystal Structure of the MYB domain of the RAD transcription factor from Antirrhinum majus. PROTEINS: Structure, Function, and Bioinformatics 65:1041-1045.

Stevenson, C. E. M., Burton, N., Costa, M., Nath, U., Dixon, R. A., Coen, E. S. and Lawson, D. M. (2005). Crystallisation and preliminary X-ray analysis of the RAD protein from Antirrhinum majus. Acta Cryst. F16: 885-888.

Crawford, B. C. W., Nath, U., Carpenter, R., and Coen, E.S. (2004). CINCINNATA controls both cell differentiation and growth in petal lobes and leaves of Antirrhinum. Plant Physiol. 135(1): 244-253.

Nath, U., Crawford, B., Carpenter, R., and Coen, E.S. (2003). Genetic control of surface curvature. Science 299, 1404-1407.