Numerous members of the third kingdom, Archaea, are extreme hyperthermophiles. Such organisms pose many interesting fundamental questions in molecular biology, since all of their life processes occur at elevated temperatures. For instance, how do regulatory proteins recognize and bind to operators at temperatures above 100 degrees C? How can the DNA replicate with high fidelity, and how do these organisms avoid excessive mutation due to heat-induced DNA lesions, and what repair strategies do they employ? We propose to develop a functional genomic analysis of one of the high temperature archaea, Pyrobaculum aerophilum, that can grow up to 104 degrees C, with an optimal growth temperature of 100 degrees C. We have sequenced and fully annotated the 2.2 mega base genome of Pyrobaculum aerophilum, and are completing the construction of microarrays containing every ORF, in collaboration with Todd Lowe at Stanford/U.C. Santa Cruz. We will carry out experiments on genome-wide gene expression in different environments, and use the data to identify coregulated genes. Through extended analyses, we hope to use the data to set up experiments to identify regulatory pathways and regulatory proteins. We will extend the development of a genetic system with the aim of being able to carry out reverse genetics in this organism. We have begun an indepth investigation of the repair systems in this organism, and we will continue to characterize DNA repair strategies and proteins.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM057917-08
Application #
6931875
Study Section
Genome Study Section (GNM)
Program Officer
Anderson, James J
Project Start
1998-08-01
Project End
2007-07-31
Budget Start
2005-08-01
Budget End
2007-07-31
Support Year
8
Fiscal Year
2005
Total Cost
$305,000
Indirect Cost
Name
University of California Los Angeles
Department
Microbiology/Immun/Virology
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Rong, Rui; Slupska, Malgorzata M; Chiang, Ju-Huei et al. (2004) Engineering large fragment insertions into the chromosome of Escherichia coli. Gene 336:73-80
Yang, Hanjing; Chiang, Ju-Huei; Fitz-Gibbon, Sorel et al. (2002) Direct interaction between uracil-DNA glycosylase and a proliferating cell nuclear antigen homolog in the crenarchaeon Pyrobaculum aerophilum. J Biol Chem 277:22271-8
Fitz-Gibbon, Sorel T; Ladner, Heidi; Kim, Ung-Jin et al. (2002) Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A 99:984-9
House, Christopher H; Fitz-Gibbon, Sorel T (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54:539-47
Yang, H; Phan, I T; Fitz-Gibbon, S et al. (2001) A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum. Nucleic Acids Res 29:604-13
Slupska, M M; King, A G; Fitz-Gibbon, S et al. (2001) Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum. J Mol Biol 309:347-60
Yang, H; Fitz-Gibbon, S; Marcotte, E M et al. (2000) Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J Bacteriol 182:1272-9
Fitz-Gibbon, S T; House, C H (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27:4218-22