Dan S. Ray, Ph.D.

Work Address:
MBI
Los Angeles, CA 90095 301A MBI
CAMPUS - 157005
CA MBI
Los Angeles, CA 90095

Affiliations
Affiliations
Professor, Microbiology, Immunology & Molecular Genetics, Molecular Biology
Member, Basic/Translational Research, Jonsson Comprehensive Cancer Center, Immunity, Microbes & Molecular Pathogenesis GPB Home Area, JCCC Cancer and Stem Cell Biology Program Area, Microbiology, Immunology & Molecular Genetics
Research Interests
The mitochondrial DNA of trypanosomes is a novel form of DNA consisting of thousands of circular DNA molecules catenated into a single enormous network termed kinetoplast DNA (kDNA). How is this network replicated and how is its replication coordinated with nuclear DNA replication during the cell cycle? What are the components of the kDNA replication machinery? What are the molecular mechanisms regulating the periodic expression of both nuclear and kinetoplast DNA replication genes? How is kDNA condensed and organized into a compact disc within the kinetoplast? These questions are being addressed in the trypanosomatid Crithidia fasciculata using molecular genetic, biochemical and immunological methods. Replication of the kDNA of Crithidia occurs in approximate synchrony with that of nuclear DNA and both nuclear and kinetoplast DNA replication genes are expressed periodically during the cell cycle. Replication proteins and their corresponding genes under investigation include the mitochondrial proteins DNA topoisomerase II, DNA ligase, structure-specific endonuclease and ribonuclease H. We are investigating the expression of these genes in synchronous cultures and identifying sequence elements required for periodic accumulation of the mRNAs. The identification of additional kDNA replication proteins and the determination of their roles in replication and their possible association with multi-protein replication complexes is also underway. Finally, we are also identifying and characterizing a group of histone-like proteins associated with the kDNA and which may play a role in the structural organization of the DNA.
Biography

The mitochondrial DNA of trypanosomes The mitochondrial DNA of trypanosomes is a novel form of DNA consisting of thousands of circular DNA molecules catenated into a single enormous network termed kinetoplast DNA (kDNA). How is this network replicated and how is its replication coordinated with nuclear DNA replication during the cell cycle? What are the components of the kDNA replication machinery? What are the molecular mechanisms regulating the periodic expression of both nuclear and kinetoplast DNA replication genes? How is kDNA condensed and organized into a compact disc within the kinetoplast? These questions are being addressed in the trypanosomatid Crithidia fasciculata using molecular genetic, biochemical and immunological methods. Replication of the kDNA of Crithidia occurs in approximate synchrony with that of nuclear DNA and both nuclear and kinetoplast DNA replication genes are expressed periodically during the cell cycle. Replication proteins and their corresponding genes under investigation include the mitochondrial proteins DNA topoisomerase II, DNA ligase, structure-specific endonuclease and ribonuclease H. We are investigating the expression of these genes in synchronous cultures and identifying sequence elements required for periodic accumulation of the mRNAs. The identification of additional kDNA replication proteins and the determination of their roles in replication and their possible association with multi-protein replication complexes is also underway. Finally, we are also identifying and characterizing a group of histone-like proteins associated with the kDNA and which may play a role in the structural organization of the DNA.

Publications

A selected list of publications:

Sinha, K. M., Hines, J. C. and Ray, D. S.   Cell Cycle-Dependent Localization and Properties of a Second Mitochondrial DNA Ligase in Crithidia fasciculata, Eukaryotic Cell, 2006; 5: 54-61.
Downey, N., Hines, J. C., Sinha, K. M., and Ray, D. S.   Mitochondrial DNA Ligases of Trypanosoma brucei, Eukaryotic Cell, 2005; 4: 765-774.
Sinha KM, Hines JC, Downey N and Ray DS   Mitochondrial DNA Ligase in Crithidia fasciculata, Proc. Natl. Acad. Sci, 2004; 101(13): 4361-4366.
Mittra, B. and Ray, D.S.   Presence of a poly (A)-binding protein and two proteins with cell cycle dependent phosphorylation in the Crithidia fasciculata mRNA cycling-sequence binding protein II. , Eukaryotic Cell, 2004; 3: 1185-1197.
Avliyakulov NK, Lukes J, Ray DS   Mitochondrial histone-like DNA-binding proteins are essential for normal cell growth and mitochondrial function in Crithidia fasciculata Eukaryotic cell. , 2004; 3(2): 518-26.
Avliyakulov NK, Hines JC, Ray DS   Sequence elements in both the intergenic space and the 3' untranslated region of the Crithidia fasciculata KAP3 gene are required for cell cycle regulation of KAP3 mRNA Eukaryotic cell. , 2003; 2(4): 671-7.
Mittra B, Sinha KM, Hines JC, Ray DS   Presence of multiple mRNA cycling sequence element-binding proteins in Crithidia fasciculata The Journal of biological chemistry. , 2003; 278(29): 26564-71.
Mahmood R, Mittra B, Hines JC, Ray DS   Characterization of the Crithidia fasciculata mRNA cycling sequence binding proteins Molecular and cellular biology. , 2001; 21(14): 4453-9.
Engel ML, Hines JC, Ray DS   The Crithidia fasciculata RNH1 gene encodes both nuclear and mitochondrial isoforms of RNase H Nucleic acids research. , 2001; 29(3): 725-31.
Mahmood R, Hines JC, Ray DS   Identification of cis and trans elements involved in the cell cycle regulation of multiple genes in Crithidia fasciculata Molecular and cellular biology. , 1999; 19(9): 6174-82.
Engel ML, Ray DS   The kinetoplast structure-specific endonuclease I is related to the 5' exo/endonuclease domain of bacterial DNA polymerase I and colocalizes with the kinetoplast topoisomerase II and DNA polymerase beta during replication Proceedings of the National Academy of Sciences of the United States of America. , 1999; 96(15): 8455-60.
Engel ML, Ray DS   A structure-specific DNA endonuclease is enriched in kinetoplasts purified from Crithidia fasciculata Nucleic acids research. , 1998; 26(20): 4733-8.
Mahmood R, Ray DS   Nuleclear extracts of Crithidia fasciculata contain a factor(s) that binds to the 5'-untranslated regions of TOP2 and RPA1 mRNAs containing sequences required for their cell cycle regulation The Journal of biological chemistry. , 1998; 273(37): 23729-34.
Hines JC, Ray DS   The Crithidia fasciculata KAP1 gene encodes a highly basic protein associated with kinetoplast DNA Molecular and biochemical parasitology. , 1998; 94(1): 41-52.
Hines JC and Ray DS   Periodic Synthesis of Kinetoplast Topoisomerase II During the Cell Cycle, Molecular and Biochemical Parasitology, 1997; 88: 249-252.
Hines JC, Ray DS   Tandem arrangement of two genes encoding kinetoplast-associated H1 histone-like proteins Molecular and biochemical parasitology. , 1997; 89(1): 41-9.
Brown LM, Ray DS   Cell cycle regulation of RPA1 transcript levels in the trypanosomatid Crithidia fasciculata Nucleic acids research. , 1997; 25(16): 3281-9.
Pasion SG, Hines JC, Ou X, Mahmood R, Ray DS   Sequences within the 5' untranslated region regulate the levels of a kinetoplast DNA topoisomerase mRNA during the cell cycle Molecular and cellular biology. , 1996; 16(12): 6724-35.
Xu CW, Hines JC, Engel ML, Russell DG, Ray DS   Nucleus-encoded histone H1-like proteins are associated with kinetoplast DNA in the trypanosomatid Crithidia fasciculata Molecular and cellular biology. , 1996; 16(2): 564-76.