Joseph P Ogas
- Associate Professor of Biochemistry
Ogas Lab page
Area of Expertise: Regulation of
cell identity, signal transduction, chromatin
The identity of
plant cells is remarkably fluid. This property
is dramatically demonstrated by the ability of
an excised piece of differentiated plant tissue
to regenerate into an entire plant. We
are interested in characterizing the factors and
mechanisms that govern plant cell identity and
facilitate its flexible nature. To accomplish
this goal, we are utilizing a mutant ofArabidopsis
thaliana, pickle (pkl),
in which the primary
root differentiates improperly and expresses
embryonic characteristics after germination. pkl
roots that express embryonic differentiation
characteristics are called pickle roots based on
their appearance. Expression of the pickle root
phenotype is dependent on gibberellin (GA), a
plant growth regulator known to promote such
diverse processes as germination, cell
elongation, and initiation of flowering.
We have cloned PKL, and it codes for a
predicted protein that is a new member of the
CHD family. The CHD proteins derive their name
from the possession of three domains: a chromo
(chromatin organization modifier) domain, a
SNF2-related helicase/ATPase domain, and a
DNA-binding domain. CHD genes are well
conserved throughout eukaryotes. Some CHD
family members, referred to as CHD3 or mi-2
proteins, contain an additional domain of
sequence homology: the PHD zinc finger. PKL
contains this domain and thus is also a CHD3
protein. CHD3 proteins from Xenopus and human
cell lines have been shown to associate with
histone deacetylase indicating that they may act
as negative regulators of
transcription. Consistent with such a role for
PKL in Arabidopsis, we have shown that LEC1,
a promoter of embryonic identity, is derepressed
in germinating pklseedlings.
The cloning of the PKL gene provides a
unique opportunity to study the intersection of
the diverse areas of GA signal transduction,
developmental identity, and chromatin
structure. Based on the phenotype of the pkl mutant
and the function of proteins that are similar to
PKL, our working model is that PKL regulates the
transcription of genes in response to
GA. Specifically, we propose that PKL
establishes transcriptional repression of
embryonic genes during germination by altering
the structure of chromatin. This model will be
tested by the following experimental
strategies: examination of the expression of PKL,
characterization of the DNA-binding site of PKL,
identification of genes that exhibit PKL-dependent
transcription, identification of proteins that
interact with PKL, and genetic screens for
mutations that affect the phenotype of pkl plants.
The intent of the proposed experiments is to
elucidate the role of PKL and to identify
factors and mechanisms that govern GA signal
transduction and developmental transitions in
plants. Insight gained from these studies may
be useful in increasing agricultural
productivity and/or in the generation of new
crops. The observation that CHD proteins are
conserved in eukaryotes suggests that the
results obtained in our studies of PKL function
in Arabidopsis may be generally applicable to
eukaryotes. Perhaps plants and animals utilize
common regulatory machinery to govern
developmental transitions. If so, the proposed
experiments with PKL in Arabidopsis may
shed light on one of the factors involved in
Awards & Honors
(2012) Outstanding Undergraduate Counselor for Biochemistry. Purdue University Department of Biochemistry.
(2010) Outstanding Counselor Award Nominee, 2009-2010. College of Agriculture.
(2009) Outstanding Counselor Award Nominee, 2008-2009. College of Agriculture.
(2008) Outstanding Counselor Award Nominee, 2007-2008. College of Agriculture.
(2005) Outstanding Undergraduate Teaching Award Nominee, 2004-2005. Department of Biochemistry.
(2004) Outstanding Service to Students Award Nominee, 2003-2004. College of Agriculture.
(2004) Outstanding Undergraduate Teaching Award Nominee. Department of Biochemistry.
Ogas, J. P. (2004). Methods and compositions for regulating developmental identity. U.S. Patent No. P-99059.00.WO. Washington, D.C.: U.S. Patent and Trademark Office.
Ogas, J. P. (2004). Sugar and lipid metabolism regulators in plants V. U.S. Patent No. P-03048300.WO. Washington, D.C.: U.S. Patent and Trademark Office.
Harmeyer, K. M., South, P. F., Bishop, B., Ogas, J. P., & Briggs, S. D. (2014). Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure. Nucleic Acids Res., pii: gku1347. Retrieved from http://nar.oxfordjournals.org/content/early/2015/01/29/nar.gku1347.full.pdf+html
Ho, K. K., Zhang, H., Golden, B. L., & Ogas, J. P. (2012). PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. Biochim. Biophys. Acta., 2, 199-210. Retrieved from http://www.sciencedirect.com/science/article/pii/S1874939912001824
Zhang, H., Bishop, B., Ringenberg, W., Muir, W. M., & Ogas, J. P. (2012). The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27. Plant Physiol., 159, 418-432. Retrieved from http://www.plantphysiol.org/content/159/1/418.full.pdf+html
Zhang, H., & Ogas, J. P. (2009). An epigenetic perspective on developmental regulation of seed genes. Mol. Plant, 2, 610-627.
Muir, W. M., Rosa, G. J. M., Pittendrigh, B. R., Xu, Z., Rider, S. D., Fountain, M., & Ogas, J. P. (2009). A mixture model approach for the analysis of small exploratory microarray experiments. Computational Statistics and Data Analysis, 53, 1566-1577.
Zhang, H., RiderJr., S. D., Henderson, J., Fountain, M., Chuang, K., Kandachar, V., . . . Ogas, J. P. (2008). The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27.. J. Biol. Chem., 283(33), 22637-22648. Retrieved from http://www.jbc.org/cgi/content/full/283/33/22637?view=long&pmid=18539592
Ogas, J. P. (2007). Preface to special issue on plant chromatin: Structure and expression. Biochim Biophys Acta, 1769, 267-8.
Muir, W. M., Romero-Severson, J., Rider, S. D., Simons, A. V., & Ogas, J. P. (2006). Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis. J Data Sci, 4, 323-341. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793414/
Li, H. C., Chuang, K., Henderson, J. T., Bai, Y., RiderJr, S. D., Zhang, H., . . . Ogas, J. P. (2005). PICKLE acts during germination to repress expression of embryonic traits. Plant Journal, 44(Part 6), 1010-1022. Retrieved from http://www3.interscience.wiley.com/journal/118705615/abstract?CRETRY=1&SRETRY=0
Rider, S. D., Hemm, M. R., Hostetler, H. A., Li, H. C., Chapple, C., & Ogas, J. P. (2004). Metabolic profiling of the arabidopsis pkl mutant reveals selective derepression of embryonic traits. Planta, 219, 480-499. Retrieved from http://springerlink.metapress.com/content/lldwr8e80dd5udl5/