Dae Kwan Ko, Ph.D.

I am an Assistant Professor - Fixed Term in the Plant Research Laboratory, the Department of Plant Biology, and the Great Lakes Bioenergy Research Center (GLBRC) at Michigan State University (MSU).

During my Ph.D. studies in the Department of Molecular Biosciences at the University of Texas at Austin, I mainly investigated the molecular mechanism of hybrid vigor, known as heterosis, in maize using an integrative approach of experimental biology and genomics.

After completing my Ph.D. studies, as a postdoc, I joined the lab of C. Robin Buell at MSU for bioinformatics training. Following the successful training, I joined the lab of Federica Brandizzi where, as a postdoc, I investigated gene regulatory mechanisms underlying responses to endoplasmic reticulum stress in plants using systems-level approaches. Particularly, I have developed coexpression network-based gene discovery pipelines and applied them to pinpointing regulatory hub genes for functional characterization.

In my current position, I investigate how genes are dynamically regulated in plants, in response to climate change using multi-omics network approaches. My research is funded by GLBRC through the Brandizzi Lab and by the MSU GREEEN project for which I serve as a PI.

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Research interests

I am an early-career researcher who is passionate about addressing critical biological questions at the systems-level with a hypothesis-driven approach using the power of genomics. Do genes and proteins interact with each other in cells as we do in society? Then, what could be the functional consequences of those interactions in regulating biological pathways? I believe that these molecular interactions, called “biological networks”, are crucial for all living organisms to maintain cellular homeostasis. My long-term research goal is toward characterizing gene networks underlying significant biological pathways and applying the findings to translational research. Representative papers are highlighted in yellow below.

An IRE1-proteasome system signaling cohort controls cell fate determination in unresolved proteotoxic stress of the plant ER
Ko DK, Kim JY, Thibault ET and Brandizzi F
Nat Plants. 2023 9:1333-1346.
Github page for scripts / Media highlight

Description: In this study, we performed a forward genetic screening and discovered a new regulator that helps cells determine life or death under unresolved ER stress. Using an interdisciplinary approach of omics, biochemistry, and genetics, we identified its working mechanism and functional relationship with existing regulators.

Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses
Ko DK, Brandizzi F
Plant Proteostasis. Methods in Molecular Biology, 2023 vol 2581. Humana, New York, NY
Github page

Description: The paper provides a step-by-step workflow for coexpression network analyses using WGCNA and discusses its potential applications.

Transcriptional competition shapes proteotoxic ER stress resolution
Ko DK and Brandizzi F
Nat Plants. 2022 May;8(5):481-490.
Github page for scripts / Media highlight

Description: We discovered a new UPR regulator and characterized its functional role in the UPR at the mechanistic level through a multi-omics approach.

Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana
Ko DK, Brandizzi F
Commun Biol. 2022 Jan 11;5(1):16.
Github page for scripts / Media highlight

Description: To better understand the transcriptional activities of the UPR master regulators, bZIP28 and bZIP60, I generated time-series transcriptome datasets and performed coexpression analyses, which allowed me to pinpoint downstream genes for functional characterization.

Bioenergy Belowground: challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production
York LM, Cumming JR, Trusiak A .... Ko DK .... Yang WH
The Plant Phenome Journal 5.1 2022: e20028.
GLBRC website

Description: In this white paper, the GLBRC colleagues and I discussed the significance and challenges of root biology in bioenergy research.

Science forum: vision, challenges and opportunities for a plant cell atlas
Plant Cell Atlas Consortium, Ghosh Jha S, Borowsky AT .... Ko DK ... Rhee SY
eLife. 2021 Sep 7;10:e66877.
Plant Cell Atlas website

Description: Plant Cell Atlas (PCA) colleagues and I reported the activities that we initiated for the plant research community.

Relevance of the Unfolded Protein Response to Spaceflight-Induced Transcriptional Reprogramming in Arabidopsis
Angelos E, Ko DK, Zemelis-Durfee S, Brandizzi F
Astrobiology. 2021 Mar;21(3):367-380.
Media highlight

Description: This study focused on investigating transcriptome changes affected by UPR regulators in space. Plants were germinated, grown, and harvested in spaceflight. As a co-author, I performed RNA-seq analyses.

A temporal hierarchy underpins the transcription factor‐DNA interactome of the maize UPR
Ko DK, Brandizzi F
Plant J. 2021 Jan;105(1):254-270.
Media highlight

Description: How the UPR is controlled is largely unknown in non-model plant species including maize. To better understand the regulatory landscape of the UPR, I performed TF network analyses based on enhanced Y1H screens for selected UPR marker genes in maize.

First plant cell atlas workshop report
Rice S, Fryer E, Ghosh Jha S...The Plant Cell Atlas Consortium (including Ko DK)
Plant Direct. 00:1–10.
Plant Cell Atlas website

Description: In this white, Plant Cell Atlas (PCA) colleagues and I report the very first workshop that was successfully held online

Network‐based approaches for understanding gene regulation and function in plants
Ko DK, Brandizzi F
Plant J. 2020 Oct;104(2):302-317.
Highlighted in the Society for Experimental Biology's Spring Bulletin

Description: Understanding gene function is a critical requirement to advance knowledge of the principles underpinning fundamental and applied plant biology. In this review, we describe predictive analyses, their strengths and pitfalls that are fast-forwarding our understanding of gene regulation and function in plants.

Functional diversification of ER stress responses in Arabidopsis
Pastor-Cantizano N, Ko DK, Angelos E, Pu Y, Brandizzi F.
Trends Biochem Sci. 2020 Feb;45(2):123-136.
On The Cover

Description: In recent years, the field of plant UPR has substantially advanced, revealing new regulators and mechanisms. My colleagues and I provide recent updates on the new development in the plant UPR to the research community.

Evaluation of Methods to Assess in vivo Activity of Engineered Genome-Editing Nucleases in Protoplasts
Nadakuduti SS, Starker CG, Ko DK, Jayakody TB, Buell CR, Voytas DF, Douches DS.
Front Plant Sci. 2019 Feb 8;10:110.

Description: We compare three existing methods for detection of gene editing activity in potato protoplasts. In this collaborative project, I performed amplicon-seq analyses as a co-author.

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation
Ko DK, Nadakuduti SS, Douches DS, Buell CR.
PLoS One. 2018 Nov 8;13(11):e0206055.

Description: We describe the impact of Agrobacterium-mediated transformation of a mutated acetolactate synthase gene on the transcriptome of potato, highlight the extent of positional effect of transgene insertion and that one component of somaclonal variation is due to altered expression of transcription factors and their downstream targets.

Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids
*Ko DK, *Rohozinski D, Song Q, Taylor SH, Juenger TE, Harmon FG, *Chen ZJ. *These authors contributed equally to this work
PLoS Genet. 2016 Jul 28;12(7):e1006197.

Description: Heterosis, or hybrid vigor, has been widely used in agriculture for more than a century. Despite extensive investigation and various models proposed, the molecular basis for heterosis remains largely elusive. I led this collaborative project to identify and characterize the molecular link of growth heterosis and the circadian clock. We report that higher carbon fixation and starch accumulation in maize hybrids than in the parents are associated with differences in the diurnal regulation of gene expression.

Genome-wide dosage-dependent and-independent regulation contributes to gene expression and evolutionary novelty in plant polyploids
Shi X, Zhang C, Ko DK, Chen ZJ.
Mol Biol Evol. 2015 Sep;32(9):2351-66.

Description: We investigate allelic expression novelties using a series of newly synthesized Arabidopsis tetraploids that contain one, two, three, and four genomes of A. thaliana or A. arenosa, as well as reciprocal crosses containing the same nuclear genomes but different cytoplasms.

Submergence-inducible and circadian rhythmic basic helix–loop–helix protein gene in Nicotiana tabacum
Ko DK, Lee MO, Hahn JS, Kim BG, Hong CB.
J Plant Physiol. 2009 Jul 1;166(10):1090-100..

Description: In my MS research, I identified and characterized a flooding stress-responsive transcription factor gene of which expression was not only responsive to flooding stress but also under the circadian clock regulation in Nicotiana. It demonstrated potential crosstalk between the clock and abiotic stress responses.

Website template courtesy of Jon Barron.