Research Faculty #20

General Information

Academic History

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

Contact Information

Office Phone
Office Location
Biological Sciences Building, Rm 2317
Lab Phone
Lab Location
Biological Sciences Building, Rm 2332

Research Information

Research Abstract

Life cycle transitions of sexual eukaryote; Molecular mechanisms of nutrient sensing in phototrophic eukaryotes; Ubiquitin-dependent mechansism for chloroplast quality control; Evolution of developmental/epigenetic mechanisms; Macroevolutionary transitions from prokaryotes to eukaryotes and from green algae to land plants; Mitigating climate change by engineering algae for efficient carbon capture and biofuel production.

Research Interests

The Experimental Model System - Chlamydomonas reinhardtii:

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.

Chlamydomonas also serves as an experimental model to explore the molecular mechanisms of nutrient sensing in photosynthetic microalgae, whose understanding will pave ways to utilizing microalgae 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 the following themes.

1. Nutrient-sensing mechanisms for photosynthetic eukaryotes (supported by NSERC-Discovery)

Understanding of transcriptional regulation governing N utilization in phototrophic eukaryotes is critical for engineering crops to improve N utilization efficiency.  In C. reinhardtiiN starvation is the only known signal to trigger sexual development.  In animals and fungi, the Target of Rapamycin (TOR) complex is the master regulator of N nutrient-dependent signal transduction, but TOR seems to play a minor role in the N starvation-induced transcriptome of C. reinhardtii.  Using forward genetic approach we recently isolated two mutant classes: nsi1-1 - 1-5 lacking any known N starvation responses in N-depleted conditions, and cns1 - cns3 showing constitutive starvation responses including N-scavenging and salvaging in N-replete conditions.  The current study is focused on elucidating how Nsi1 senses N-depletion and regulates Cns1-3 and identifying Nsi1 interaction partners using genetic and biochemical approaches.  Our pioneering study in algae will stimulate comparable studies in plants, investigating N-dependent signaling pathways in plants.

Team 1 Members: Yuan, Jack, Sunjoo, Moyan, Cindy 

2. What are the benefits and consequences of sex?: A driver of developmental mechanisms (supported by NSERC-Discovery)

Developmental gene regulatory networks were first described for the hierarchical relationships among transcription factors that direct organ/tissue/cell-type specifications and have expanded to include epigenetic mechanisms. The genomes of complex multicellular and simple unicellular organisms differ in the number and kind of transcription factors but display comparable complexity in putative epigenetic mechanisms.  Many studies have attempted to identify the biological functions of epigenetic pathways in unicellular organisms but have failed to show notable roles in growth or stress tolerance, prompting a critical question: how and why did complex epigenetic mechanisms evolve early in eukaryotic history?

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 focuses on the elucidation of gene regulatory networks driven by these homeobox proteins.

Team 2 Members: Thamali and Sunjoo

3. How do eukaryotes control live and death of organelles?: Ubiquitin-dependent mechanisms for chloroplast quality control (supported by STAIR)

Most sexually reproducing eukaryotes receive their organellar DNA from a single parent, a process termed uniparental inheritance.  In C. reinhardtii, the uniparental inheritance of the chloroplast genome is accomplished by selective degradation of the chloroplast DNA derived from a gamete that lacks the MTL-plus locus, suggesting that the genetic determinant that specifies protection from degradation is linked to MTL-plus.  We have identified the OTU2P cluster residing in the MTL-plus as the plus determinant for protecting chloroplast DNAs from degradation.  OTU2P encodes a deubiquitinating enzyme in the C65-protease family.  We are currently investigating the molecular mechanism of chloroplast DNA degradation/ recycling and testing a mechanical link between Otu2P and the Chloroplast-associated ubiquitin-mediated degradation pathway.  This query will elucidate the mechanisms involved in the quality control of chloroplast, directly regulating the copy number of organellar genomes.

Team 3 Members: Sunjoo and Thamali

4. Exploring the green potential of photosynthesis: Algal breeding using quantitative genetics (supported by NSERC-Discovery)

Mutations fuel evolution but also impose limits on habitat expansion and organismal complexity, requiring cells to invest in mechanisms that guard genomic integrity.  Meiosis provides multiple means of shuffling/correcting mutations: chromosomal recombination, gene conversion, and potentially mutagenic repair synthesis, all dependent on double-strand DNA breaks, which might have contributed to the benefit of sex. To quantify the role of sex in short-term evolution, we investigate the role of meiosis in correcting mutations and those of candidate molecular players regulating cross-overs and gene conversions with single-cell genomics approach.  Available self-fertile strains present an excellent platform for quantifying the rate of mutation correction during meiosis in the absence of polymorphism between parental genomes.  The quantitative understanding of the meiotic effect will provide the basis of experimental evolution studies that are focused on investigating the role of meiosis in adaptive evolution under stressors using mutagenized strains before and after the meiosis.

The resilience of green algae that survive through tremendous changes on earth in the last billion years may suggest robust evolutionary strategies.  Such a strategy will help to develop algal strains that can be deployed in extreme and unusual environments outside standard growth conditions.  A detailed understanding of the meiotic process will guide us to search for the possible phenotypes quickly via laboratory evolution experiments.  This expedited evolutionary approach will save time and money associated with directed engineering strategies.  The resultant strains with robust characteristics will provide algae-based solutions for mitigating the current climate crisis.

Team 4 Members: Nolan and Thamali

5. Go-Green: Opening the new era of green photosynthetic living nanofabric for sustainable future (supported by NFRF-Exploration). 

The world is facing one of the biggest environmental challenges threatened by the unbalanced release of carbon dioxide (CO2) from burning fossil fuels and deforestation. Increase in the atmospheric greenhouse gases has driven climate changes. Reducing the reliance on non-renewable resources has been the focus of global efforts to mitigate climate change. However, recent 2015 Paris agreement urged that the reversal of the current climate change requires direct efforts of converting CO2 into resources. The goal of this research is to provide a proof-of-concept that can potentially overcome the primary barriers to implement biological CO2 conversion solutions by introducing photosynthetic living organisms into a nano-scale fabric.

Microalgae refer to microscopic photosynthetic organisms free-living in ocean and soil, and responsible for approximately half of the atmospheric oxygen and up to 50% of the total CO2 fixation on earth. Microalgae are considered as a sustainable solution to mitigate climate change for their efficient photosynthesis and wide-range of application. Microalgae have been utilized to treat waster water or exhaust gas while producing feedstock for biofuels and high-value compounds used for food supplements, pharmaceutical, and cosmetics. Despite such promises, the application of microalgae for CO2 capture has been limited by existing methods relying on large-scale cultures such as open ponds and liquid-holding containers. Global utilization of microalgae requires innovative technology to mobilize them to harsh conditions and remote places.

Our project aims to generate green nanomaterial capturing live photosynthetic cells. This green nanomaterial can be readily tailored in various forms and a wide range of scales. Recent advances of nanotechnology offer solutions and ideas for synthesizing hybrid polymers combining nanoparticles and living cells, whose exploration is so far limited. Taking advantage of the great flexibility and adaptation of microalgae to grow in diverse environments, we propose a pioneering project that produces a prototype of microalgae-nanofiber. This prototype will be capable of natural CO2 capture and conversion to biomass with oxygen production, whereby it is readily deployable. If successful, its manufacturing will offer indoor/outdoor CO2-conversion systems for waste gas or water treatment and for medical application such as wound-healing patches that supply oxygen and antibiotics.

Team 5: Under recruitment

Funding Sources:

NSERC-Discovery (2012-2019, 2019-)
NFRF-Exploration (2020-): collaboration with F. Ko (UBC, F of Applied Science)
STAIR (2020): collaboration with T. Mayor (UBC, F of Medicine)

CFI (2013-2018)
URSA fellowship (2012, 2013, 2014, 2015, 2016)
NSF (2011-2015): collaboration with A. Worden (MBARI)
KCRC (2012-2017): collaboration with SJ. Sim (Korea U.), ES. Jin (Hanyang U.), NL. Jeon (Seoul Natl. U.)

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)
Nolan Shelley (Graduate, MSc candidate)
Moyan Jia (Graduate, MSc candidate)
Cindy Shi (Undergraduate, Directed study)

Former members

Evan Cronmilller (Graduate, MSc 2017): Biotech. Employee
Michelle (Ming Hsiu) Wang (Graduate, MSc 2015): Lecturer
Sangsuk Pak (Graduate, visiting  scholar, 2012-2013): Research Associate
Touzard Anaelle (Graduate, visiting scholar, 2013): Biotech. Employee

Ki Min Lee (Technician, 2014-2015): Reseach Technician
Andrew Papadopoli (Graduate, MSc candidate, 2012)


Anna Jiwon Song (Work study 2018)
Julia Shu (Work study, 2018)
Amelia He (Work study, 2018)
Jenny Lee (Directed study/Work study, 2016-2018): UBC graduate school
Ariel (Nai Chun) Shao (NSERC fellow, 2016): UBC Dentistry
Vivian Shao (Work study, 2016)
John Lee (Work study, 2016-2017)
Lana (Ran Ha) Hong (Co-op/NSERC fellow, 2015,2016): UBC Medical School
Emilia Hurtado (Directed study, 2015-2016)
Jeff Chen (NSERC fellow, 2016)
Amy Zhang (FoS summer fellow, 2014): Biotech. Employee
Grace Chew (Work study, 2014-2015)
Saif Akkad (NSERC fellow, 2016): Medical School
Alex Akdikmen (Work study, 2014-2015)
Joyce Wang (Work study, 2014)
Ally Gao (Co-op/Directed study, 2014): Biotech. Employee
Jennifer Cheung (Directed study)
Bethanie Giang (Work study, 2015): UBC Medical School
Deepak Toor (Co-op/NSERC fellow, 2012): Medical School
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): North Dakoda, Ph.D. candidate

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

Dong-yoon Choi (2016), Gain Choi (2017), Eunhwa Bae (2017), Jung Ho Choi (2018), Narae Kang (2018), Sae-Eun Roh (2019), Noh Hyung Jin (2019)

Scientific Opportunities

1. Funded PhD/MSc positions available in Molecular Cell Biology

We are looking for one or two Ph.D./M.Sc. students to join our research team starting from fall 2020 or winter 2021
The student projects will involve molecular genetics experiments in Chlamydomonas; biochemistry experiments focused on protein-protein and protein-substrate interaction; genome-wide analysis of chromatin structures/gene expression.
An academic background in Molecular geneticsBiochemistry, or Developmental cell biology is required. Biology students with a strong interest in bioinformatics or developmental evolution are encouraged to apply.

Please send the following application material by email.

a. statement of interest/motivation letter
b. CV
c. Selected publications
d. contact information of 2 or more referees

Available projects are in the following area: gene regulatory mechanisms during sexual development, organellar genome quality control, and nitrogen sensing and signaling mechanisms. Details should be referred to as the above research interests section and recent publications.

2. Undergraduates who seek research experience are welcomed to contact us regarding available opportunities.

Selected Publications

Munz, J., Xiong Y., Kim, J.Y.H., Sung, Y.J., Seo, S.-B., Hong, R.H., Kariyawasam, T., Shelley, N., Lee, J.,  Sim, S.J., Jin, ES., and Lee, J.-H. (2020) Arginine-fed culture generates triacylglycerol by triggering nitrogen starvation responses during robust growth in Chlamydomonas. Algal Res. 46:101782. (link to the paper)

Cronmiller E., Toor D., Shao N.C., Kariyawasam T.,Wang M.H., and Lee, J.-H. (2019) Cell wall integrity signaling regulates cell wall-related gene expression in Chlamydomonas reinhardtii. Sci. Rep.9:12204.

Kariyawasam, T., Joo, S., Lee, J., Toor, D., Gao, A.F., Noh, K.-C., and Lee, J.-H. (2019) TALE homeobox heterodimer GSM1/GSP1 is a fail-safe switch that prevents unwarranted genetic recombination in Chlamydomonas reinhardtii. Plant J. 100:938-953, doi: 10.1111/tpj.14486.

Goodenough, U., Heiss, A., Roth, R., Rusch, J., and Lee, J.-H.(2019) Acidocalcisomes: Ultrastructure, biogenesis, and distribution in microbial eukaryotes. Protist. 170:287-313.

Price, D.C., Goodenough, U.W., Roth, R., Lee, J.-H.Kariyawasam, T., Mutwil, M., Ferrari, C., Facchinell, F., Ball, S.G., Cenci, U., Chan, C.X., Yoon, H.S., Weber, A.P.M., and Bhattacharya, D. (2019) Analysis of an improved Cyanophora paradoxagenome assembly. DNA Research. dsz009.

Kariyawasam, T., Joo S., Goodenough U., and Lee, J.-H. (2019) Novel approaches for generating and manipulating diploid strains of Chlamydomonas reinhardtii. Algae 34:35-43.

Joo, S.$, Wang, M.H.$, Lui, G.,Lee, J., Barnas, A., Kim, E., Sudek, S., Worden, A.Z., and Lee, J.-H. (2018) Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Viridiplantae. BMC Biology 16:136. ($: equally contributed)

Goodenough, U.W., Roth, R., Kariyawasam, T., He, A., and Lee, J.-H. (2018) Epiplasts: Membrane skeletons and epiplastin proteins in Euglenids, Glaucophytes, Cryptophytes, Ciliates, Dinoflagellates, and Apicomplexans. mBio 9:e02020-18.

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, ES., 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.