Center for Gene Regulation in Health and Disease (GRHD)

Hee-Sook Kim

Overview

Trypanosoma brucei is a protozoan parasite that causes African sleeping sickness in humans and a similar disease in livestock, mainly in sub-Saharan Africa. T. brucei cycles between the insect vector (tsetse fly) and mammalian hosts. In the mammalian host, the parasite expresses a single species of surface coat protein (VSG, variant surface glycoprotein) at any given time, while having over 2000 VSG genes in the genome – known as the ‘VSG silencing’ (all VSGs are transcriptionally repressed, except one). To clear the parasite, the host immune system recognizes the expressed VSG and kills the parasite. However small populations of parasites escape the host immune killing by expressing a different subset of VSG genes – a process known as ‘VSG switching’. Therefore, T. brucei’s immune evasion via antigenic variation requires precisely controlled VSG silencing and switching mechanisms. Genome integrity factors play important roles in T. brucei antigenic variation, and my lab is interested in how DNA replication, transcription and chromatin structure factors talk to each other to control antigen gene diversification and to maintain genome integrity.

DNA replication, transcription and chromatin structure: Transcription in T. brucei occurs polycistronically, and start and stop sites of transcription are marked by specific chromatin modifications. Transcription termination sites (TTSs) are marked specifically by histone variants, H3v and H4v, and a Kinetoplastid-specific DNA modification, base J. I have discovered that simultaneous deletion of these TTS marks caused severe transcription defects and replication problems. Interestingly, depletion of MCM-BP (Kim et al, 2013 PLOS ONE), a replication protein, shares similar phenotypes as the chromatin mark mutants (unpublished data). My lab is interested in investigating how specific chromatin marks and chromatin structure changes can affect DNA replication as well as transcription. We are using high-throughput sequencing approaches as well as genetic and proteomic techniques.

Developing large-scale screening tools: T. brucei antigenic variation shares mechanistic features with many classic monoallelic gene expression systems both in pathogenic and non-pathogenic organisms. To find novel factors, I also focused on developing various genetic tools for large-scale screens. Recently, I have generated the first T. brucei overexpression library in collaboration with Drs. Nina Papavasiliou (DKFZ/University of Heidelberg), Christine Clayton (ZMBH/University of Heidelberg), Galadriel Hovel-Miner (George Washington University), and Danae Shulz (Harvey Mudd College). This overexpression library is a new resource in the field that can be used to identify novel factors via gain-of-function phenotypes. I am currently working on several screening projects using this library as well as previously described RNAi libraries.

Collaborators: I am collaborating with Dr. Nina Papavsiliou at DKFZ and the University of Heidelberg for library generation/screening as well as VSG structure projects, and Dr. Bibo Li at CSU for the DNA replication and telomere maintenance project.

List of Published Work in MyBibliography:

Publications

1.     Schulz D, Zaringhalam M, Papavasiliou FN and Kim HS** (2016) Base J and H3.V regulate transcriptional termination in Trypanosoma brucei. PLOS Genetics 12(1):e1005762 PMID: 26796638 (** last and corresponding)

2.     Schulz D, Mugnier MR, Paulsen EM, Kim HS, Chung CW, Tough DF, Rioja I, Prinjha RK, Papavasiliou FN, and Debler EW (2015) Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome PLoS Biol. 13(12):e1002316. PMC4672894

3.     Cross GAM, Kim HS, and Wickstead B (2014) Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427. Molecular Biochemical Parasitology. doi: 10.1016 PMID: 24992042 “PMC Journal – In Process”

4.     Kim HS*, Li Z, Boothroyd C, and Cross GAM (2013) Strategies to construct null and conditional null Trypanosoma brucei mutants using Cre-recombinase and loxP. Molecular Biochemical Parasitology 191(1):16-19. PMC3830529 (*corresponding)

5.     Benmerzouga I, Concepcion-Acevedo J, Kim HS*, Vandoros AV, Cross GA, Klingbeil MM and Li B (2013) Trypanosoma brucei Orc1 is essential for nuclear DNA replication and affects both VSG silencing and VSG switching. Molecular Microbiology 87: 196-210. PMC3535549  (*co-first author)

6.     Kim HS*, Park S-H, Günzl A, and Cross GA (2013) MCM-BP is required for repression of life-cycle specific genes transcribed by RNA polymerase I in the mammalian infectious form of Trypanosoma brucei. PLoS ONE 8(2):e57001.  PMC3581582  (*corresponding)

7.     Kim HS and Cross GAM (2011) Identification of Trypanosoma brucei RMI1/BLAP75 homologue and its roles in antigenic variation. PLoS ONE 6(9):e25313. PMC3182221

8.     Kim HS and Cross GA (2010) TOPO3a influences antigenic variation by monitoring Expression-Site-associated VSG switching in Trypanosoma brucei. PLoS Pathogens Jul 8; 6(7):e1000992  PMC2900300

9.     Kim HS, Vijayakumar S, Reger M, Harrison J, Haber JE, Weil C, and Petrini JH (2008) Functional interactions between Sae2 and the Mre11 complex. Genetics 178, 711-723 PMC2248341

10.  Kim HS and Brill, SJ (2003) MEC1-dependent phosphorylation of yeast RPA1 in vitro. DNA Repair 2(12), 1321-35 PMID: 14642562 “PMC Journal – In Process”

11.  Bae KH, Kim HS, Bae SH, Kang HY, Brill S, and Seo YS (2003) Bimodal interaction between replication-protein A and Dna2 is critical for Dna2 function both in vivo and in vitro. Nucleic Acids Research 31(12), 3006-15 PMC162255

12.  Kim HS and Brill, SJ (2001) Rfc4 interacts with Rpa1 and is required for both replication and DNA damage checkpoints in Saccharomyces cerevisae. Molecular Cellular Biology 21(11), 3725-37 PMC87010