Our lab is interested in the molecular biology and physiology of the Archaea. The Archaea have a distinct evolutionary position, separate from Bacteria and Eukarya, and possess a mosaic of molecular properties. To better understand the unique physiology of the archaeal cell, we are examining two systems where there is a close relationship to eukaryal processes: transcription regulation and the maturation of stable RNAs. We are also interested in the comparative genome analysis and the evolutionary events that have shaped extant archaeal genomes.
Transcription and gene regulation
We have recently used a genome-wide tiled array to analyze the transcriptome of the halophilic archaeon, Haloferax volcanii. These studies have identified genes expressing during balanced growth, as well as changes in the transcriptome in response to nutrient starvation, stationary phase and salt stress. This work has also revealed changes in the RNA levels of many transcription factors; most notably, the general transcription factors, TBP and TFB, and transcription factors associated with amino acid degradation pathways. Gene expression studies are continuing with genetic analysis of regulatory gene mutants and the development of in vitro approaches to examine the molecular aspects of their action.
Maturation of stable RNA transcripts
Studies on the processing of tRNA introns in the Archaea have led us, and others, to the discovery that Archaea share many aspects of stable RNA processing with systems present in eukaryal cells. We are continuing studies on the relationship between tRNA intron splicing and C/D box snoRNA-guided methylation using the tRNATrp tRNA of H. volcanii as a model system. We have extended these studies to examine the role of the K-turn binding protein, L7ae, which is a component of the C/D box sno-ribonucleoprotein complexes and other RNP complexes in the cell. The overall goal of these studies is to define the relationships between transcription, intron splicing and modification of stable RNAs in the Archaea.
The wealth of microbial genome sequences is providing a rich data set for the comparative analysis of archaeal and bacterial genomes. We continue to participate in genome sequencing studies of the haloarchaea with a focus toward understanding the evolutionary events that accompanied the emergence of the haloarchaeal from the methanogen lineage. We are especially interested in genes that were acquired by lateral gene transfer and how these genes have been assimilated into the regulatory schemes and physiology of their new host.
- Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T & Eisen JA (2010). The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One. 19, e9605 (1-20).
- Ray WC, Ozer HG, Armbruster DW & Daniels CJ. (2009) Beyond identity- when classical homology searching fails, why, and what you can do about it. Bioinformatics, 2009, Ohio Collaborative Conference: 51-6.
- Kirkland PA, Humbard MA, Daniels CJ & Maupin-Furlow JA. (2008) Shotgun proteomics of the haloarchaeon Haloferax volcanii. J Proteome Res. 11, 5033-9.
- Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ & Li H. (2003) Structure and function of archaea Box C/D sRNP core proteins. Nat Struct Biol. 10, 256-63.