Dr. Hwan Youn Homepage

Youn Lab

Hwan Youn

Professor

Degree

Ph.D., 1998, Seoul National University

Postdoctoral Research

University of Wisconsin-Madison

Address

Department of Biology

College of Science & Mathematics

Fresno State

2555 E. San Ramon Ave. M/S SB73

Fresno, CA 93740-8034

Phone: 1-559-278-8305

Fax: 1-559-278-3963

E-mail: hyoun@csufresno.edu

Office/ lab: S314B/ S313

My Research

Bacteria are everywhere on earth. Their omnipresence is due to their adaptation to environmental cues, which relies on specialized sensing mechanisms for environmental changes. The CooA/CRP/FNR family of transcription factors sense all kinds of ligands, including oxygen, carbon monoxide, nitric oxide, and metabolites like a-ketoglutarate and aromatic compounds, thereby helping bacteria express specific genes necessary for environmental/ nutritional changes. The structural motif for this versatile CooA/CRP/FNR family is rather simple: each member has two domains (N-terminal ligand-binding domain and C-terminal DNA-binding domain) connected by a long C-helix component. These proteins act as dimers.

My recent work has focused on two members of this family: CooA and CRP. CooA is the CO (carbon monoxide)-dependent, heme-containing transcriptional activator in Rhodospirillum rubrum. CRP is the cAMP receptor protein that senses the absence of a particular carbon source, glucose, in Escherichia coli by responding to the intracellular level of cAMP, thereby regulating the expression of carbon metabolism-related genes. My scientific question has been how the conformations of these proteins are changed by ligand binding in the context of DNA binding and what are the critical components in the signaling pathway for each protein.

Interestingly, some of the proteins of this family are known to function as virulence factors in human pathogens such as Listeria monocytogens, Pseudomonas aeruginosa, and others. Many critical details are yet to be learned such as their cognate ligands and their cellular targets for regulation. My intention is to apply current knowledge of CooA/CRP/FNR protein family to the homologs in the pathogens in order to understand their role during the process of pathogenesis.

Publications

41. Lee SH, Youn H, Kang SG, Lee HS (2019) Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1. J. Microbiol. 57:138-142.

40. Ji CJ, Yang YM, Kim JH, Ryu SH, Youn H, Lee JW (2018) The roles of two O-donor ligands in the Fe2+-binding and H2O2-sensing by the Fe2+-dependent H2O2 sensor PerR. Biochem. Biophys. Res. Commun. 501:458-464.

39. Hicks MN, Gunasekara S, Serate J, Park J, Mosharaf P, Zhou Y, Lee JW, Youn H (2017) Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction. J. Microbiol. 55:816-822.

38. Kim JH, Yang YM, Ji CJ, Ryu SH, Won YB, Ju SY, Kwon Y, Lee YE, Youn H, Lee JW (2017) The instability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression. J. Microbiol. 55:457-463.

37. Kim JH, Ji CJ, Ju SY, Yang YM, Ryu SH, Kwon Y, Won YB, Lee YE, Youn H, Lee JW (2016) Bacillus licheniformis contains two more PerR-like proteins in addition to PerR, Fur, and Zur orthologues. PLoS One 11(5):e0155539.

36. Gunasekara SM, Hicks MN, Park J, Brooks CL, Serate J, Saunders CV, Grover SK, Goto JJ, Lee JW, Youn H (2015) Directed evolution of the Escherichia coli cAMP receptor protein at the cAMP pocket. J. Biol. Chem. 290:26587-26596.

35. Ji CJ, Kim JH, Won YB, Lee YE, Choi TW, Ju SY, Youn H, Helmann JD, Lee JW. (2015) Staphylococcus aureus PerR is a hypersensitive hydrogen peroxide sensor using Fe-mediated histidine oxidation. J. Biol. Chem. 290:20374-20386.

34. Ryu M-H, Youn H, Kang I-H, Gomelsky M (2015) Identification of bacterial guanylate cyclases. Proteins 83:799-804.

33. Kim M, Choi AR, Lee SH, Bae SS, Yang T, Jeon JH, Lim JK, Youn H, Kim TW, Lee HS, Kang SG (2015) A novel CO-responsive transcriptional regulator and enhanced H2 production by an engineered Thermococcus onnurineus NA1. Appl. Environ. Microbiol. 81:1708-1714.

32. Benabbas A, Karunakaran V, Youn H, Poulos TL, Champion PM (2012) Effect of DNA binding on germinate CO recombination kinetics in the CO-sensing transcription factor, CooA. J. Biol. Chem. 287:21729-21740.

31. Karunakaran V, Benabbas A, Youn H, Champion PM (2011) Vibrational coherence spectroscopy of the heme domain in the CO-sensing transcriptional activator CooA. J. Am. Chem. Soc. 133:18816-18827.

30. Serate J, Roberts GP, Berg O, Youn H (2011) Ligand responses of Vfr, the virulence factor regulator from Pseudomonas aeruginosa. J. Bacteriol. 193:4859-4868.

29. Lee AJ, Clark RW, Youn H, Ponter S, Burstyn JN (2009) Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA. Biochemistry 48:6585-6597.

28. Marvin KA, Kerby RL, Youn H, Roberts GP, Burstyn JN (2008) The transcription regulator RcoM-2 from Burkholderia xenovorans Is a cysteine-ligated hemoprotein that undergoes a redox-mediated ligand switch. Biochemistry 47:9016-9028.

27. Youn H, Koh J, Roberts GP (2008) Two-state allosteric modeling suggests protein equilibrium as an integral component for cyclic AMP (cAMP) specificity in the cAMP receptor protein of Escherichia coli. J. Bacteriol. 190:4532-4540.

26. Kerby RL, Youn H, Roberts GP (2008) RcoM: a new single-component transcriptional regulator of CO metabolism in bacteria. J. Bacteriol. 190:3336-3343.

25. Ibrahim M, Kuchinskas M, Youn H, Kerby RL, Roberts GP, Poulos TL, Spiro TG (2007) Mechanism of the CO-sensing heme protein CooA: New insights from the truncated heme domain and UVRR spectroscopy. J. Inorg. Biochem. 101:1776-1785.

24. Youn H, Kerby RL, Koh J and Roberts GP (2007) A C-helix residue, Arg123, has important roles in both the active and inactive forms of the cAMP receptor protein. J. Biol. Chem. 282:3632-3639.

23. Clark RW, Youn H, Lee AJ, Roberts GP and Burstyn JN (2007) DNA binding by an imidazole-sensing CooA variant is dependent on the heme redox state. J. Biol. Inorg. Chem. 12:139-146.

22. Youn H, Conrad M, Chung SY and Roberts GP (2006) Roles of the heme and heme ligands in the activation of CooA, the CO-sensing transcriptional activator. Biochem. Biophys Res. Commun. 348:345-350.

21. Ibrahim M, Kerby RL, Puranik M, Wasbotten IH, Youn H, Roberts GP and Spiro TG (2006) Heme displacement mechanism of CooA activation: mutational and Raman spectroscopic evidence. J. Biol. Chem. 281:29165-29173.

20. Youn H, Kerby RL, Conrad M and Roberts GP (2006) Study of highly constitutively active mutants suggests how cAMP activates cAMP receptor protein. J. Biol. Chem. 281:1119-1127.

19. Youn H, Thorsteinsson MV, Conrad M, Kerby RL and Roberts GP (2005) Dual roles of an E-helix residue, Glu167, in the transcriptional activator function of CooA. J. Bacteriol. 187:2573-2581.

18. Roberts GP, Kerby RL, Youn H and Conrad M (2005) CooA, a paradigm for gas sensing regulatory proteins. J. Inorg. Biochem. 99:280-292.

17. Clark RW, Youn H, Parks RB, Cherney MM, Roberts GP and Burstyn JN (2004) Investigation of the role of the N-terminal proline, the distal heme ligand in the CO sensor CooA. Biochemistry 43:14149-14160.

16. Roberts GP, Youn H and Kerby RL (2004) CO-sensing mechanisms. Microbiol. Mol. Biol. Rev. 68:453-473.

15. Youn H, Kerby RL and Roberts GP (2004) Changing the ligand specificity of CooA, a highly specific heme-based CO sensor. J. Biol. Chem. 279:45744-45752.

14. Puranik M, Nielsen SB, Youn H, Hvitved AN, Bourassa JL, Case MA, Tengroth C, Balakrishnan G, Thorsteinsson MV, Groves JT, McLendon GL, Roberts GP, Olson JS and Spiro TG (2004) Dynamics of carbon monoxide binding to CooA. J. Biol. Chem. 279:21096-21108.

13. Youn H, Kerby RL, Conrad M and Roberts GP (2004) Functionally critical elements of CooA-related CO sensors. J. Bacteriol. 186:1320-1329.

12. Coyle CM, Puranik M, Youn H, Nielsen SB, Williams RD, Kerby RL, Roberts GP and Spiro TG (2003) Activation mechanism of the CO sensor CooA. Mutational and resonance Raman spectroscopic studies. J. Biol. Chem. 278:35384-35393.

11. Kerby RL, Youn H, Thorsteinsson MV and Roberts GP (2003) Repositioning about the dimer interface of the transcription regulator CooA: a major signal transduction pathway between the effector and DNA-binding domains. J. Mol. Biol. 325:809-823.

10. Youn H, Kerby RL and Roberts GP (2003) The role of the hydrophobic distal heme pocket of CooA in ligand sensing and response. J. Biol. Chem. 278:2333-2340.

9. Youn H, Kerby RL, Thorsteinsson MV, Clark RW, Burstyn JN and Roberts GP (2002) Analysis of the L116K variant of CooA, the heme-containing CO sensor, suggests the presence of an unusual heme ligand resulting in novel activity. J. Biol. Chem. 277:33616-33623.

8. Youn H, Kerby RL, Thorsteinsson MV, Conrad M, Staples CR, Serate J, Beack J and Roberts GP (2001) The heme pocket afforded by Gly117 is crucial for proper heme ligation and activity of CooA. J. Biol. Chem. 276:41603-41610.

7. Thorsteinsson MV, Kerby RL, Youn H, Conrad M, Serate J, Staples CR and Roberts GP (2001) Redox-mediated transcriptional activation in a CooA variant. J. Biol. Chem. 276:26807-26813.

6. Thorsteinsson MV, Kerby RL, Conrad M, Youn H, Staples CR, Lanzilotta WN, Poulos TL, Serate J and Roberts GP (2000) Characterization of variants altered at the N-terminal proline, a novel heme-axial ligand in CooA, the CO-sensing transcriptional activator. J. Biol. Chem. 275:39332-39338.

5. Youn H and Kang SO (2000) Enhanced sensitivity of Streptomyces seoulensis to menadione by superfluous lipoamide dehydrogenase. FEBS Lett. 472:57-61.

4. Cho SH, Na JU, Youn H, Hwang CS, Lee CH and Kang SO (1999) Sepiapterin reductase producing L-threo-dihydrobiopterin from Chlorobium tepidum. Biochem. J. 340:497-503.

3. Youn H, Kwak J, Youn HD, Hah YC and Kang SO (1998) Lipoamide dehydrogenase from Streptomyces seoulensis: biochemical and genetic properties. Biochim. Biophys. Acta 1388:405-418.

2. Cho SH, Na JU, Youn H, Hwang CS, Lee CH and Kang SO (1998) Tepidopterin, 1-O-(L-threo-biopterin-2'-yl)-beta-N-acetylglucosamine from Chlorobium tepidum. Biochim. Biophys. Acta 1379:53-60.

1. Youn HD, Youn H, Lee JW, Yim YI, Lee JK, Hah YC and Kang SO (1996) Unique isozymes of superoxide dismutase in Streptomyces griseus. Arch. Biochem. Biophys. 334:341-348.

Lab member

· Hwan Youn: PI

· Edgar Gutierrez: graduate student (Biology)

· Amanda Rea: graduate student (Biology)

· Daisy Pacheco: graduate student (Biology)

· Lawrence De Vera: graduate student (Biology)

· Ramanpreet Kaur: undergraduate student (Biology)

· Marcus Carranza: undergraduate student (Biology)

· Former members

Teaching

2020

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

· Hot Topics Seminar (Biol 260T), Department of Biology, Fresno State

· Microbioal Genetics (Biol 153), Department of Biology, Fresno State

· Biology Colloquium (Biol 280), Department of Biology, Fresno State

2019

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

· Microbioal Genetics (Biol 153), Department of Biology, Fresno State

· Seminar in Biological Science (Biol 281), Department of Biology, Fresno State

2018

· Genetics (Biol 102), Department of Biology, Fresno State

Textbook: Essentials of Genetics

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Genetics (Biol 102), Department of Biology, Fresno State

Textbook: Essentials of Genetics

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms_14th Ed

· Microbioal Genetics (Biol 153), Department of Biology, Fresno State

2017

· Genetics (Biol 102), Department of Biology, Fresno State

Textbook: Essentials of Genetics

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Molecular Biology 2 (Biol 241B), Department of Biology, Fresno State

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms_14th Ed

· Microbioal Genetics (Biol 153), Department of Biology, Fresno State

2016

· Genetics (Biol 102), Department of Biology, Fresno State

Textbook: Essentials of Genetics

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Biology Colloquium (Biol 189T and BIol 280), Department of Biology, Fresno State

· Molecular Biology 2 (Biol 241B), Department of Biology, Fresno State

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms_14th Ed

· Microbioal Genetics (Biol 153), Department of Biology, Fresno State

2015

· Molecular Biology 1 (Biol 241A), Department of Biology, Fresno State

· Molecular Biology (Biol 150), Department of Biology, Fresno State

Textbook: Molecular Biology of the Gene

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Molecular Biology 2 (Biol 241B), Department of Biology, Fresno State

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms

2014

· Molecular Biology 2 (Biol 241B), Department of Biology, Fresno State

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms

2013

· Molecular Biology 1 (Biol 241A), Department of Biology, Fresno State

Textbook: Lewin's Genes XI

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Microbiology (Biol 120), Department of Biology, Fresno State

Textbook: Brock Biology of Microorganisms

· Bioinformatics (Biol 151), Department of Biology, Fresno State

2012

· Functional Genomics (Biol 260T), Department of Biology, Fresno State

Textbook: Microbial Functional Genomics and others

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Nucleic Acid Technology Lab (Biol 243), Department of Biology, Fresno State

Textbook: From Genes to Genomes

· Seminar in Cellular and Molecular Biology (Biol 181), Department of Biology, Fresno State

2011

· Functional Genomics (Biol 260T), Department of Biology, Fresno State

Textbook: Microbial Functional Genomics and others

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Nucleic Acid Technology Lab (Biol 243), Department of Biology, Fresno State

Textbook: From Genes to Genomes

2010

· Molecular Biology 1 (Biol 241A), Department of Biology, Fresno State

Textbook: Molecular Biology of the Gene

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· General Microbiology Lab (Biol 120 Lab), Department of Biology, Fresno State

· Microbiology Journal Club (Biol 189T), Department of Biology, Fresno State

Flyer: MJC-2010

· Nucleic Acid Technology Lab (Biol 243), Department of Biology, Fresno State

Textbook: From Genes to Genomes

2009

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Nucleic Acid Technology Lab (Biol 243), Department of Biology, Fresno State

Textbook: The Condensed Protocols From Molecular Cloning: A Laboratory Manual

2008

· Microbial Physiology (Biol 160), Department of Biology, Fresno State

Textbook: The Physiology and Biochemistry of Prokaryotes

· Seminar in Biological Science (Biol 281), Department of Biology, Fresno State

2007-2008

· HHMI Teaching Fellow, University of Wisconsin-Madison

Education

Ph.D., Microbiology, Seoul National University, South Korea, 1998

M.S., Microbiology, Seoul National University, South Korea, 1993

B.S., Microbiology, Seoul National University, South Korea, 1991

Professional experiences

2019-present: Professor, Department of Biology, Fresno State

2014-2019: Associate Professor, Department of Biology, Fresno State

2008-2014: Assistant Professor, Department of Biology, Fresno State

2002-2008: Assistant Scientist, Department of Bacteriology, University of Wisconsin-Madison

(PI: Dr. Gary P. Roberts)

2000-2002: Postdoctoral Fellow, Department of Bacteriology, University of Wisconsin-Madison

(PI: Dr. Gary P. Roberts)

1998-2000: Postdoctoral Fellow, RCMM, Seoul National University, South Korea