Charles J. Daniels

daniels.7@osu.edu

Molecular Biology of the archaea: archaeal SNO-RNAs.

Although Archaea are prokaryotes, they possess a number of molecular characteristics that are most closely related to those present in eukaryal cells. Two notable examples of this close relationship are the archaeal transcription apparatus, which is similar to eukaryal RNA polymerase II (RNAPII), and the enzymes involved in tRNA maturation. Understanding the molecular mechanisms of these processes and how these systems relate to the physiology of the halobacteria are the focus of our current research.

Transcription in the Halophilic Archaea: In addition to the presence of the eukaryal RNAPII-like complex, the halophilic Archaea are distinct in having multiple copies of the general transcription factor genes, TATA Binding Protein (TBP) and Transcription Factor B (TFB). For example, we have identified and characterized 4 TBP and 10 TFB encoding genes in Haloferax volcanii. This unusual level of complexity appears to be restricted to the halophilic genera of the Archaea; it is not observed in other Archaea or in eukaryal cells. We have also established that the transcription of these individual TBP and TFB genes is regulated and that the pattern of regulation suggests coordinate expression of specific TBP-TFB pairs. While this scheme is reminiscent of multiple sigma factors in bacterial cells, it represents a novel expansion of the eukaryal RNAPII type transcription system. To further explore this system we are using a combination of in vitro biochemical and in vivo genetic techniques to investigate the mechanisms of protein-protein and protein-DNA interactions and the consequences of these interactions on global gene expression and the physiology of the cell.

tRNA maturation: As an extension to our continuing interest in tRNA intron splicing in the Archaea, we have recently initiated studies on the role of snoRNA-like RNAs in the maturation of stable RNA precursors in H. volcanii. Initial studies indicate that the highly conserved H. volcanii tRNATrp intron functions as a eukaryal-like C/D box small nucleolar RNA (snoRNA), directing 2'-O-methylation at two positions in the mature tRNATrp RNA. We have also characterized the genes encoding fibrillarin and Nop5, two of the protein components of the eukaryal small nucleolar ribonucleoprotein (snoRNP) complex. The presence of snoRNPs in the Archaea, and their absence in the Bacteria, illustrates another close affiliation between the eukaryal nucleus and the Archaea. We are currently investigating the assembly of snoRNPs in H. volcanii and the interplay between intron removal and snoRNA-dependent modification during the maturation of tRNATrp.

Genome Analysis: Over the past several years we have participated in the annotation and analyses of two completed archaeal genome sequences, Methanobacterium thermoautotrophicum and Halobacterium NRC-1. More recently we have begun a new collaboration to analyze the genome sequence of H. volcanii, which is the model organism for our biochemical and physiological studies. Through these studies we hope to better define the biochemical and evolutionary relationships between the archaeal information processing systems and their eukaryal nuclear counterparts. In addition to developing strategies for incorporating Bioinformatics-based analyses in our research, we are working with the Ohio Supercomputer Center to bring Bioinformatics tools to a statewide user group.

Ray, W.C., Munson, R.S. Jr. and Daniels, C.J. Tricross:Using dot-plots in sequence to detect uncataloged inter genic features. Bioinformatics in press.

Ray, W.C. and Daniels, C.J. 2001 The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis. Bioinformatics 17 100-104.

Ng,W.V., et. al. 2000. Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. U.S.A. 97:12176-12181.

Baliga , N.S., Y.A. Goo, V.W. Ng, L. Hood, C.J. Daniels and S. DasSarma. 2000. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol. Micro. 36:1184-1185.

Thompson DK, Palmer JR, Daniels C.J. 1999. Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii. Mol. Microbiol. 33(5):1081-92.

Thompson, D.K. and Daniels, C.J. 1998. Heat-shock inducibility of an archaeal TATA-like promoter element is controlled by adjacent sequence elements. Mol. Micro. 27:541-51

Palmer, J.R. and Daniels, C.J. 1994. A transcriptional reporter for in vivo promoter analysis in the archaeon Haloferax volcanii. Appl. Environ. Micro. 60: 3867-3869.

Douglas R. Smith, et al. 1997. Sequence of the Methanobacterium thermoautotrophicum strain DH genome: archaeal methanogenesis, bacterial metabolic and eucaryal information processing pathways. J. Bacteriol. 179:7135-55.

Kuo, Y-P., Thompson, D.K., St. Jean, A., Charlebois, R.L. and Charles J. Daniels. 1997. Characterization of Two Heat Shock Genes from Haloferax volcanii: A Model System for Transcription Regulation in the Archaea. J. Bacteriol. 179:6318-6324

Reeve, J.N., Sandman, K. and Daniels, C.J. 1997. Archaeal histones, nucleosomes, and transcription initiation. Cell 89: 999-1002.

Kleman-Leyer, K., D.A. Armbruster, and C.J. Daniels. 1997. Properties of the H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell 89: 839-847.

Armbruster, D.W. and Daniels, C.J. 1997. Splicing of intron-containing tRNATrp by the archaeon Haloferax volcanii occurs independent of mature tRNA structure. J. Biol. Chem. 272: 19758-19762.

Palmer, J.R. and Daniels, C.J. 1995. In vivo definition of an archaeal promoter. J. Bacteriol. 177: 1844-1849.