Smalle, Jan

Research Overview and Computational Needs

Principal Investigator: Dr. Jan A. Smalle

Department: Plant and Soil Sciences, University of Kentucky

Email: jsmalle@uky.edu

PhD Students: Timothy E. Shull, Sumudu Karunadasa

Staff: Dr. Jasmina Kurepa

Group Activities

Our research group conducts plant molecular biology research with two primary areas of interest.

Cytokinin Signaling^1-5

Our labs main research interest is the role of the plant hormone cytokinin in plant growth and development. Our research projects involve uncovering the molecular mechanisms underpinning the orchestration of protein synthesis through cytokinin signaling, the influence of phenylpropanoid metabolism on the cytokinin response pathway, and proteolytic control of cytokinin signaling components. Another area of our research involves research into the influence of allelochemicals on plant hormone signaling, which is motivated by the development of novel agricultural biotechnologies. 

Nanoparticle and Plant Interactions^6-9

The second major focus of our research efforts is uncovering potential applications for plant based nanotechnology, with a focus on ultra-small anatase TiO₂ nanoparticles. More specifically, we use TiO₂ nanoparticles in order to harvest flavonoids from living plant tissue. This is made possible by the high affinity of the anatase TiO₂ surface for compounds containing catechol functional groups, which flavonoids are especially enriched in. Upon cellular nanoparticle uptake, this high affinity allows in vivo binding of flavonoids. The nanoparticle-flavonoid conjugates are then extruded from the plant cell, and the flavonoids isolated on the nanoparticle surface can then be removed. Currently, two focal points of this project are understanding the plant stress responses involved in this process as well as uncovering other uses for this technology.

Projects with Computational Needs

Cytokinin Signaling

We will be using the computing cluster primarily to analyze publicly available genomic and transcriptomic datasets in order to inform our research on cytokinin signal transduction. Primarily, we will be assembling draft genomes and transcriptomes of plants which are known to produce various categories of allelochemicals and conducting a comparative analysis of genes central to the cytokinin signaling network in plants with different allelochemical profiles. The ultimate goal of this research is to uncover potential pathways to allelochemical resistance by analyzing the molecular mechanisms used by plants to remain unaffected by their own secondary metabolites. In addition to this analysis, we will be using publicly available datasets to inform our wet-lab research pertaining to the evolution of cytokinin signaling networks in higher plants.

Personnel:

Timothy E. Shull

Computational methods:

De novo genome and transcriptome assembly, read processing, read mapping, annotation, and differential expression analysis

Software:

Trinity, Trinotate, RSEM, Bowtie, R, fastx_toolkit, FastQC, ncbi-blast, TransDecoder, STAR, sratoolkit, sqlite-tools, RNAMMER, hmmsearch2

All software used is publicly available (free) to download online, and those programs not available on the LCC will be installed as needed on the individual students working directories.

Collaborators and Students:

N/A

Grants:

Key Publications:

1. Kurepa, J.; Shull, T. E.; Smalle, J. A., Antagonistic activity of auxin and cytokinin in shoot and root organs. Plant Direct 2019, 3, (2), e00121.
2. Kurepa, J.; Li, Y.; Smalle, J. A., Cytokinin signaling stabilizes the response activator ARR1. The Plant journal : for cell and molecular biology 2014, 78, (1), 157-68.
3. Kurepa, J.; Li, Y.; Perry, S. E.; Smalle, J. A., Ectopic expression of the phosphomimic mutant version of Arabidopsis response regulator 1 promotes a constitutive cytokinin response phenotype. BMC plant biology 2014, 14, 28.
4. Smalle, J.; Kurepa, J.; Yang, P.; Babiychuk, E.; Kushnir, S.; Durski, A.; Vierstra, R. D., Cytokinin growth responses in Arabidopsis involve the 26S proteasome subunit RPN12. The Plant cell 2002, 14, (1), 17-32.
5. Kurepa, J.; Shull, T. E.; Karunadasa, S. S.; Smalle, J. A., Modulation of auxin and cytokinin responses by early steps of the phenylpropanoid pathway. BMC plant biology 2018, 18, (1), 278.
6. Shull, T. E.; Kurepa, J.; Smalle, J. A., Anatase TiO2 Nanoparticles Induce Autophagy and Chloroplast Degradation in Thale Cress (Arabidopsis thaliana). Environmental science & technology 2019, 53, (16), 9522-9532.
7. Kurepa, J.; Nakabayashi, R.; Paunesku, T.; Suzuki, M.; Saito, K.; Woloschak, G. E.; Smalle, J. A., Direct isolation of flavonoids from plants using ultra-small anatase TiO(2) nanoparticles. The Plant journal : for cell and molecular biology 2014, 77, (3), 443-53.
8. Wang, S.; Kurepa, J.; Smalle, J. A., Ultra-small TiO₂ nanoparticles disrupt microtubular networks in Arabidopsis thaliana. Plant, cell & environment 2011, 34, (5), 811-20.
9. Kurepa, J.; Paunesku, T.; Vogt, S.; Arora, H.; Rabatic, B. M.; Lu, J.; Wanzer, M. B.; Woloschak, G. E.; Smalle, J. A., Uptake and distribution of ultrasmall anatase TiO2 Alizarin red S nanoconjugates in Arabidopsis thaliana. Nano Lett 2010, 10, (7), 2296-302.

Patents: