Jae-Hyeok Lee

Faculty Profile

Faculty Profile

Assistant Professor

Molecular genetics of sexual development in green algae, focusing on gene regulatory networks and cell wall assembly; Phylogenomics study of developmental mechanisms for the evolution of land plants from their green algal ancestors; Genetic engineering of algae for efficient carbon capture and biofuel production.

Ph.D. Plant Biology (2007), Washington Univ.
Postdoctoral Researcher (2007-2011), Washington Univ.

Contact Information

Biological Sciences Building, Rm 2327
Biological Sciences Building, Rm 2332

Research Interests

Main Themes:

Photosynthetic eukaryotes, collectively referred to as "algae", are the main focus of our lab. We are interested not only in how they have shaped the world as we now know it, but also in developing them for useful societal applications. Of the various algal groups, we work primarily on the green algae because they are 1) of ancient (> 1 billion years ago) origin, 2) widely distributed (i.e. marine/freshwater, polar/tropical), and 3) ancestral to the land plants, a diverse group of very crucial importance to the Earth's terrestrial ecosystem. By more closely studying the genetics and development of the green algae, we hope to understand how they have adapted to new environments since their ancient phylogenetic origin, and thus survived as a group for as long as they have, developing sophisticated multicellular body plans along the way.

To this end, we have selected Chlamydomonas reinhardtii as a model for studying green algal developmental programs, and how they are controlled in the context of environmental changes. As a unicellular eukaryote, Chlamydomonas as a system is fully equipped with all of the core biological features of all eukaryotes, sharing a large portion of its genetic make-up with the land plants. For these reasons, we believe Chlamydomonas to be an ideal system to address critical evolutionary questions, such as the role of sexuality in eukaryotic evolution and the emergence of land plants.

In addition to its role as a useful evolutionary model system, Chlamydomonas also serves as an experimental model to explore the potential of photosynthetic microalgae as a sustainable resource for the capture of atmospheric carbon, and its conversion to commercially useful compounds such as biofuel and antioxidants.  Our research on the process of cellular differentiation will guide the development of algal strains useful for these purposes, in the hopes of mitigating the current crisis of anthropogenic climate change due to excessive carbon emission from fossil fuel use.

Major Research Projects:

The aims of our current research is to better understand the molecular/genetics basis of sexual development involving gamete and zygote differentiation, as long-term survival strategy during extensive nitrogen starvation. Major research activities are organized into three following groups.

1. High-throughput functional genomics:

By combining high-efficiency genetic transformation (as a method of random mutagenesis) and high-throughput screening, this team is responsible for the discovery of mutations affecting development, light harvesting, and stress response. These mutants are proving a useful resource for the investigation of the molecular details of microalgal development and productivity.

Team 1 Members: Yuan (photosynthesis), Jack (N-responses) Thamali (Development), Evan (Cell walls)

2. Algae-plant evolution:

The transition from green algae to land plants coincides with the extension of the diploid phase as the multicellular stage of the plant life cycle. A group of homeobox-containing transcription factors have been implicated in the control of life cycle transitioning within various green algal groups. This team's focus is on the elucidation of functional networks involving these homeobox proteins through the use of transcriptome analysis and yeast-2-hybrid experiments. Overall, their aim is to shed light on the evolutionary history leading to the origin of land plants.

Team 2 Members: Sunjoo (Uniparental inheritance) and Thamali (Development)

3. Quantitative genetics:

Natural populations of Chlamydomons show significant genetic variation, which may be responsible for the phenotypic differences and post-zygotic sexual incompatibility among each other. Using the recombinant progeny of these natural isolates, this team will focus on 1) genome-wide association (GWAS) of photosynthetic activity in the context of various stressful conditions and 2) the phenotypic variation due to genetic interaction between organellar and nuclear genomes.

Team 3 Members: Thamali (Recombinant progeny) and Nolan (Bioinformatics)

Funding Source
NSERC-Discovery (2012-)
URSA fellowship (2012, 2013, 2014, 2015, 2016)
NSF (2011-2015)
KCRC (2012-2017)


BIOL 260 - Fundamentals of Physiology, Plant Sections (2011, 2012 S)
BIOL 338 - Introduction to Genomics (2014, 2015, 2016 S)
BIOL 436 - Integrated Functional Genomics (2012, 2013, 2016, 2017 W)

Team Members

Current members

Sunjoo Joo (Ph.D., Research Associate)
Yuan Xiong (Graduate, PhD candidate)
Jack Munz (Graduate, PhD candidate)
Thamali Kariyawasam (Graduate, PhD candidate)
Evan Cronmilller (Graduate, MSc candidate)
Nolan Shelley (Graduate, MSc candidate)
Jenny Lee (Undergraduate, Directed study/Work study)
Amelia He (Undergraduate, Volunteer)

Former members

Michelle (Ming Hsiu) Wang (Graduate, MSc 2015): Lecturer
Ki Min Lee (Technician, 2014-2015): Reseach Technician
Sangsuk Pak (Graduate, visiting  scholar, 2012-2013): Research Associate
Touzard Anaelle (Graduate, visiting scholar, 2013)
Andrew Papadopoli (Graduate, MSc candidate, 2012)

Ariel (Nai Chun) Shao (NSERC fellow, 2016)
Vivian Shao (Work study, 2016)
John Lee (Work study, 2016-2017)
Lana (Ran Ha) Hong (Co-op/NSERC fellow, 2015,2016)
Emilia Hurtado (Directed study, 2015-2016)
Jeff Chen (NSERC fellow, 2016)
Amy Zhang (FoS summer fellow, 2014)
Grace Chew (Work study, 2014-2015)
Saif Akkad (NSERC fellow, 2016)
Alex Akdikmen (Work study, 2014-2015)
Joyce Wang (Work study, 2014)
Ally Gao (Co-op/Directed study, 2014)
Jennifer Cheung (Directed study)
Bethanie Giang (Work study, 2015): UBC Medical School
Deepak Toor (Co-op/NSERC fellow, 2012)
Gary Lui (Directed study/NSERC fellow, 2012-2013)
David Kong (FoS summer fellow, 2013)
Renee Siu (Undergraduate, Directed study/Work study, 2011-2012)
Elaine Au (Undergraduate, Directed study/Work study, 2012)
Alice Chen (Undergraduate, Work study, 2013)
Jordan Sugie (Undergraduate, Directed study, 2012): Queens Medical School
Andrew Barnas (Undergraduate, Work study, 2012)

Andrea Zhu (2013), Julie van Baardwijk (2013), Lucy Chen (2013), Kayla Judson (2017)

Dong-yoon Choi (2016), Gain Choi (2017), Eunhwa Bae (2017)

Scientific Opportunities

Our laboratory is constantly looking for enthusiastic people who share interests in algal biology at all stages of their careers.
1. Post-doctoral fellows trained in molecular genetics and/or systems biology are encouraged to contact us for available positions.
2. We have one position open for graduate students in 2018W term. Students interested in joining our lab should send an inquiry with your CV and personal statement for further consideration.
3. Undergraduates who seek research projects or want laboratory experience are always welcomed to contact us regarding available opportunities.


Alex Worden (Monterey Bay Aquarium Research Institute): Oceanography focused on prasinophytes
David Baulcombe (Cambridge Univ.): Epigenetic mechanisms
Eonseon Jin (Hanyang Univ.): Microalgal photosynthetic efficiency
Olivier Vallon (IBPC, Paris): Molecular genomics tools, photosynthesis
Sabeeha Merchant (UCLA): Chlamydomonas functional genomics
Sang Jun Sim (Korea Univ.): Microfluidic devices and commercial application of microalgal productivity
Ursula Goodenough (Washington Univ.): Cell wall networks, Origin of eukaryotic cell structures
Yoshiki Nishimura (Kyoto Univ.): Nucleoid dynamics and uniparental mechanism

Selected Publications

Joo, S, Nishimura, Y., Cronmiller, E., Hong, R.H., Kariyawasam, K., Wang, M.H., Shao, N.C., Akkad, S.E., Suzuki, T., Higashiyama, T., Jin, E., and Lee, J.-H. (2017)  Gene regulatory networks for the haploid-to-diploid transition of Chlamydomonas reinhardtii. Plant Physiol. 175, 314-332.

Kim, J.Y.H., Kwak, H.S., Sung, Y.J., Choi, H.I., Hong, M.E., Lim, H.S., Lee, J.-H., Lee, S.Y., and Sim, S.J. (2016) Microfluidic high-throughput selection of microalgal strains with superior photosynthetic productivity using competitive phototaxis. Sci.Rep. 6, 21155.

Takahashi, H., Schmollinger, S., Lee, J.-H., Schroda, M., Rappaport, F., Wollman, F.-A., and Vallon, O. (2016) The PETO protein interacts with other effectors of cyclic electron flow in Chlamydomonas. Mol.Plant 9, 558-568.

Lee, J.-H., Heuser, J.E., Roth, R., and Goodenough, U. (2015) Eisosome ultrastructure and evolution in fungi, microalgae, and lichens. Euk.Cell 14, 1017-1042.

Park, J.W., Na, S.C., Nguyen, T.Q., Paik, S.-M., Kang, M., Hong, D., Choi, I.S., Lee, J.-H., and Jeon, N.L. (2015) Live cell imaging compatible immobilization of Chlamydomonas reinhardtii in microfluidic platform for biodiesel research. Biotech. Bioeng. 112, 494-501

Goodenough, U., Blaby, I., Casero, D., Gallaher, S.D., Goodson, C., Johnson, S., Lee, J.-H., et al. (2014) The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Euk.Cell 13, 591-613.

Park, S., Lee, Y., Lee, J.-H., and Jin, ES. (2013). Expression of the high light-inducible Duneliella LIP promoter. Planta 238, 1147-1156.

Cuvelier, M.L., Allen, A.E., Monier, A., McCrow, J.P., Messie, M., Tringe, S.G., Woyke, T., Welsh, R.M., Ishoey, T.,
Lee, J.-H., Binder, B.J., Latasa, M., Guigand, C., Buck, K.R., Dupont, C.L., Hilton, J.A., Thiagarajan, M., Caler, E., Lasken, R.S., Chavez, F.P., and Worden, A.Z. (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci U S A 107, 14679-14684.

Worden, A.Z., Lee, J.-H., Mock, T., Rouzé, P. Simmons, M.P., Aerts, A.L., Allen, A.E., Cuvelier, M.L., Derelle, E., Everett, M.V. et al. (2009). Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324, 268-272.

Lee, J.-H., Lin, H., Joo, S. and Goodenough, U. W. (2008). Early sexual origins of homeoprotein heterodimerization and evolution of the plant KNOX/BELL family. Cell 133, 829-840.

Lee, J.-H., Waffenschmidt, S., Small, L., and Goodenough, U. W. (2007). Between-species analysis of short-repeat modules in cell-wall and sex-related hydroxyproline-rich glycoproteins of Chlamydomonas. Plant Physiol. 144, 1813-1826.

Goodenough, U. W., Lin, H., and Lee, J.-H. (2007). Sex determination in Chlamydomonas. Seminars in Cell and Developmental Biology. 18, 350-361.