Biography

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Kim Orth

Investigator, HHMI

Professor, Department of Molecular Biology

HHMI, University of Texas Southwestern Medical Center

5323 Harry Hines Blvd. Room# NA5-120F,

Dallas, Texas, 75390-9148.

email: kim.orth@utsouthwestern.edu

Office Phone: 214-648-1685; FAX: 214-648-1488

 

Personal Statement
My laboratory is very active in elucidating mechanisms used by virulence factors expressed by bacterial pathogens. Studies using microbial genetics, biochemistry, cell biology and bioinformatics on effectors from Yersinia and Vibrio have uncovered many mechanisms that bacteria use to subvert host signaling pathways, including the discovery of two novel post translational modifications: YopJ Ser/Thr Acetylation and VopS AMPylation. We continue to study virulence mechanisms used by Vibrio parahaemolyticus T3SSs. My program has been ideal for training students and fostering new and creative ideas using rigorous methodology and analysis to test hypothesis driven basic science research. We also invest in satellite programs analyzing environmental Vibrios, metazoan AMPylation, rice blast and cancer cell exosomes. Over the years, I have contributed to varies programs for “Woman in Science”, including panel discussions for woman at American Society for Biochemistry and Molecular Biology (2017,2018), group discussion at Gordon Research Conference on Microbial Toxins and Pathogenesis (2018) and group sessions at FASEB meetings (2015, 2017, 2019 and in the future 2021). For my ASBMB Merck Award (2018), I wrote a solicited, personal reflection on my path in science for the Journal of Biological Chemistry to provide tools for younger scientists. This year, in light of COVID-19, I helped co-host two virtual international meetings: VibriOnline, May, 2020 and AMPylationPlus, July, 2020.

 

Positions and Honors
1985-1986         Master Student, Dept. Bio. Chem., UCLA School of Medicine

1987–1990        Research Associate, HHMI & UT Southwestern Medical Center

1991-1995         Ph.D. Student/Postdoctoral Fellow, UT Southwestern Med. Center

1995-2001         Postdoc Fellow and Research Inv., Dept. Bio. Chem., Univ. of Mich.

2001-2007         Assistant Professor, Dept. Molecular Biology, UT Southwestern Med. Center

2007–2011        Associate Professor, Dept. Molecular Biology, UT Southwestern Med. Center

2010-present     Secondary Appointment, Department of Biochemistry, UTSWMC

2011-present     Professor, Dept. of Molecular Biology, UT Southwestern Med. Center

2015-present     Investigator, Howard Hughes Medical Institute

 

Other Experiences and Professional Memberships

Rev. Board Editor: eLife, PNAS; Referee for Journals: Science, Nature Journals, Cell Journals, PNAS, JBC, PLoS Journals, mBio, I&I, Molecular Microbiology, Cellular Microbiology, Journal of Bacteriology

Beckman External Review 2013-2020, Beckman, Scientific Advisory Council 2020-2025,

AAAS; 2001- ASBMB; 2002- ASCB; 2006- ASM;

NIH Study Section-SEP, IDM ‘04,’09, ’10, ’11, 12’, MIST, permanent member ‘12-‘17.

 

Honors and Awards

1986                          NIH Predoctoral Training Grant, Cell and Molecular Biology. UCLA

1998-2001                 Walther Cancer Institute, Dawson Research Fellowship

2001-present              W.W. Caruth Jr. Scholar in Biomedical Research

2003-2006                  Arnold and Mabel Beckman Young Investigator Award

2006-2013                  Burroughs Wellcome Investigator in Pathogenesis of Infectious Disease

2010                           Welch Foundation Norman Hackerman Award in Chemical Science

2011                            TAMEST; 2011 Edith & Peter O’Donnell Award in Science

2012                            ASBMB Young Investigator Award

2013                            Earl A. Forsythe Chair in Biomedical Science

2016                            Elected to the American Academy of Microbiology

2018                            ASBMB Merck Award

2019                            Nirit and Michael Shaoul Visiting Scholar, Tel Aviv University

2020                            Elected to the National Academy of Sciences

2020                            Member, The Academy of Medicine, Engineering and Science of Texas

2021-2023                          American Society of Microbiology Distinguish Lecturer

 

Contributions to Science
1. Discovering a strategy to decipher biochemical mechanism used by bacterial effectors

After starting my independent research laboratory, we discovered that Yersinia YopJ uses acetylation to inhibit signaling pathways. Using an in vitro system, we found that YopJ inhibited MKKs and IKKβ by acetylating serine and threonine residues within the kinase activation loops. Acetylation of these residues by YopJ prevented their subsequent phosphorylation and inactivated them. This work is one of the first examples of a competitive post-translational modification where one modification (acetylation), directly competes for another (phosphorylation). We also demonstrated the YopJ-like homologues encode similar enzymatic activities. This discovery is important because our work on YopJ is proof of principle that effectors aid in discovery of new regulatory mechanisms. Additionally, we observe bacterial effectors perform novel chemistries. Their diversity obscures bioinformatics predictions; biochemistry is crucial to determine enzymatic activity. Most importantly, we discovered a successful strategy for elucidating the molecular mechanisms used by bacterial effectors to manipulate and disrupt host signaling pathways: find its target, determine MW change and elucidate activity.

 

  1. Broberg, C. A., Zhang, L.L., Gonzalez, H., Laskowski-Arce, M.A. & Orth, K. (2010) A Vibrio Effector Protein is an Inositol Phosphatase and Disrupts Host Cell Membrane Integrity. Science 329:1660-2.

B.Yarbrough, M., Li, Y., Kinch, L.N., Grishin, N.V., Hall B.E., & Orth, K. (2009) AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science 323: 269-272. (Epub, Nov. 2008).

C.Trosky, J.E., Li, Y., Mukherjee, S., Keitany, G., Ball, H. & Orth, K. (2007) VopA Inhibits ATP binding by Acetylating the Catalytic Loop of MKKs. Biol. Chem. 282: 34299-305. PMID:17881352

D.Mukherjee, S., Keitany, G., Li, Y., Wang, Y., Hall, B.E., Goldsmith, E. & Orth, K. (2006) Yersinia YopJ Acetylates and Inhibits Kinase Activation by Preventing Phosphorylation. Science 312:1211-14. PMID:16728640

 

  1. Orchestrated killing of one host cell in 3 hours by 3 bacteria

Sequencing of V. parahaemolyticus revealed the existence two pathogenicity islands that encode two Type III Secretion Systems (T3SS). The first system, T3SS1, is associated with all strains of the bacterium and is proposed to be essential for providing a selective advantage in the environment. We have demonstrated that the T3SS1 effectors work in concert to orchestrate a multifaceted and temporally regulated host cell infection by inducing autophagy, cell rounding, and then cell lysis. By establishing this profile of orchestrated killing, we were able to move forward and decipher the molecular mechanisms of the effectors secreted by the T3SS1 (next section).

 

Peng, W., Fernandez, J., Casey, A. K., Servage, K. A., Chen, Z., Li, Y., Tomchick, D.R. & Orth, K. Unique virulence mechanism for Vibrio effector revealed by cryo-EM structures of VopQ in complex with V-ATPase. Nat Struct Mol Biol (2020) May 18. doi: 10.1038/s41594-020-0429-1. PMID: 32424347

De Nisco, N.J., Kanchwala, M., Li, P., Fernandez, J., Xing, C. & Orth, K. (2017) Cytotoxic Vibrio T3SS1 Rewires Host Gene Expression to Subvert Cell Death Signaling and Activate Cell Survival Networks. Sci Signal May 16;10(479). pii: eaal4501. doi: 10.1126/scisignal.aal4501

Salomon D., Guo, Y., Kinch, L.N., Grishin, N.V., Mirzaei, H. & Orth, K. (2013) Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides. Nature Communications 4:2973. PMID: 24346350

Burdette, D., Seemann, J. & Orth, K. (2009) Vibrio VopQ Induces PI3-Kinase Independent Autophagy and Antagonizes Phagocytosis. Microbiol. 73:639-49. PMC:2733864

 

  1. Uncovering biochemical activities of T3SS1 effectors

We elucidated the biochemical mechanisms for three of the T3SS1 effectors using the methodology we developed while discovering the molecular mechanism of YopJ; we identify the target of the effector, assess how the target has changed, and then decipher the molecular mechanism used by the effector to cause this change. VopQ, injected as a soluble protein, binds to the V-ATPase and inserts itself into the lysosomal membrane forming an 18Å, outward rectifying channel. VopQ neutralizes this acidic compartment and prevents vacuolar fusion leading to an accumulation of autophagosomes during the first hour of infection. A second effector, VPA0450, is an inositol phosphatase that disrupts host cell membrane integrity by hydrolyzing PI(4,5)P2. The third effector, VopS, was found to encode a Fic domain that mediates a novel post-translation modification called AMPylation on small Rho GTPases. This inhibitory modification results in rounding of the infected cell.

 

Moehlman, A.T., Casey, A.K., Servage, K., Orth, K.*& Krämer, H.* Regulation of the Unfolded Protein Response by BiP AMPylation protects photoreceptors from light-dependent degeneration. eLife (2018) Jul 17:7. Pii:e38752. doi:10.7554/eLife.38752. PMID: 30015618 *co-contributing

Casey, A.K., Moelman, A., Zhang, J., Servage, K., Kramer, H. & Orth, K. Fic-mediated deAMPylation of BiP is not dependent on homo-dimerization and rescues toxic AMPylation in flies. J Biol Chem. (2017) 292 (51) pg 21193-21204

Woolery, A.R., Yu, X., LaBaer, J. & Orth, K. (2014) AMPylation of Rho GTPases subverts multiple host signaling processes. Biol. Chem. 289:32977-88. PMC4239643

Sreelatha, A., Bennett, T.L., Zheng, H., Jiang, Q.X., Orth, K.*, & Starai, J.* (2013) Vibrio VopQ forms a gated outward rectifying channel that disrupts host ion homeostasis. PNAS USA 110:11559-64. PMC:3710849

 

  1. Vibrio parahaemolyticus is a facultative intracellular pathogen: survival and proliferation inside the host cell and cytotoxicity mediated from outside the host cell.

parahaemolyticus is a globally disseminated Gram-negative marine bacterium and the leading cause of seafood-borne acute gastroenteritis. Pathogenic bacterial isolates a second T3SS (T3SS2) which is considered to be the main virulence factor in mammalian hosts. For many decades, V. parahaemolyticus has been studied as an exclusively extracellular bacterium. However, the recent characterization of the T3SS2 effector protein VopC demonstrated that this pathogen has the ability to invade, survive, and replicate within epithelial cells. The remarkable molecular aspect of this system is that it can use the same T3SS to invade and replicate inside the host cell and to cause cytotoxicity from outside the host cell. The manipulation of host signaling is quite impressive as the host cells hardly change morphology over the course of infection. We are only beginning to understand the molecular mechanisms used by effectors to manipulate the host cell.

 

Chimalapati, S.*, de Souza Santos, M.*, Lafrance, A., Ray, A., Lee, W-R., Rivera-Cancel, G., Vale, G., Pawłowski, K., Mitsche, M., McDonald, J.G. , Liou, J. & Orth, K. Vibrio deploys a Type 2 secreted lipase to esterify cholesterol with host fatty acids and mediate T3SS2-mediated cell egress. *contributed equally eLife (2020) Aug 18;9:e58057. doi: 10.7554/eLife.58057  PMCID: PMC7434443

Yang, H.*, de Souza Santos, M.*, Lee, J., Law, H.T., Chimalapati, S., Verdu, E.F., Orth, K. #, and Vallance, B.A.# A novel mouse model of enteric Vibrio parahaemolyticus infection reveals the T3SS2effector VopC plays a key role in tissue invasion and gastroenteritis. *contributed equally, #co-corresponding. mBio (2019) 17;10(6). pii: e02608-19. doi: 10.1128/mBio.02608-19.

de Souza Santos, M., Salomon, D. & Orth, K. (2017) T3SS effector VopL inhibits the host ROS response, promoting the intracellular survival of Vibrio parahaemolyticus. PLoS Pathogens (2017) 13(6): e1006438.

Li, P., Rivera-Cancel, G., Kinch, L.N., Salomon, D., Tomchick, D. R., Grishin, N.V., & Orth, K. Bile salt receptor complex activates pathogenic Type III secretion system. eLife (2016) 5:e15718

Complete List of Published Work in My Bibliography:

http://www.ncbi.nlm.nih.gov/pubmed/?term=orth+k

 

 

 

 

 

 

Ongoing Research Support

 

1 R35 GM134945-01 (Orth, Kim-PI)                                                                               02/1/20 - 01/31/25

NIH/GM

Biochemistry, biology and diversity of Fic domains 

The goal of this MIRA application is to continue our studies on the role of Fic domain containing proteins in a variety of species including mice, flies, bacteria and fungi.

I-1561 (Orth, Kim-PI)                                                                                                                                 6/01/06 - 5/31/21

Welch Foundation

Elucidate the biochemical mechanism used by Vibrio VopQ to induce autophagy.

The goal of this study is to elucidate the molecular mechanism of this effector to block autophagic flux by neutralizing the lysosome and preventing vacuolar fusion.

 

 

 

Education

Undergraduate
Texas A&M University (1984), Biochemistry
Graduate School
Uni of California (UCLA) (1986), Biochemistry
Graduate School
Univ of Tx Southwestern Med Ct (1993), Molecular Biology

Research Interest

  • Biochemistry
  • Cellular Signaling
  • Molecular Microbiology

Publications

Featured Publications LegendFeatured Publications

Beth Levine M.D. Prize in Autophagy Research.
Vitetta ES, Cobb MH, Hobbs HH, Hooper L, Morrison SJ, Orth K, Pfeiffer J, Rosen MK, Takahashi JS, Wang T, Autophagy 2021 Aug 1
Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women.
Ebrahimzadeh T, Kuprasertkul A, Neugent ML, Lutz KC, Fuentes JL, Gadhvi J, Khan F, Zhang C, Sharon BM, Orth K, Li Q, Zimmern PE, De Nisco NJ, Life Sci Alliance 2021 07 4 7

Honors & Awards

  • American Society of Microbiology Distinguish Lecturer
    (2021-2023)
  • Elected to the National Academy of Sciences
    (2020)
  • Member, The Academy of Medicine, Engineering and Science of Texas
    (2020)
  • Nirit and Michael Shaoul Visiting Scholar, Tel Aviv University
    (2019)
  • ASBMB Merck Award
    (2018)
  • American Academy of Microbiology
    Fellow (2016)
  • HHMI
    Investigator (2015)
  • Earl A. Forsythe Chair in Biomedical Science
    (2013)
  • ASBMB Young Investigator Award
    (2012)
  • TAMEST; 2011 Edith & Peter O'Donnell Award in Science
    (2011)
  • The Welch Foundation Norman Hackerman Award in Chemical Research
    (2010)
  • Burroughs Wellcome Investigator in Pathogenesis of Infectious Disease
    (2006)
  • Arnold and Mabel Beckman Young Investigator Award
    (2003)
  • W.W. Caruth, Jr. Scholar in Biomedical Research, UTSWMC
    (2001)