Research Interests

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.

Archaeal genomes

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.

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Recent Publications

Charles J. Daniels, Lien B. Lai, Tien-Hao Chen and Venkat Gopalan. Both kinds of RNase P in all domains of life: surprises galore. 2019 RNA 25: 286-291. Klyczek KK, Jacobs-Sera D, Adair TL, Adams SD, Ball SL, Benjamin RC, Bonilla JA, Breitenberger CA, Daniels CJ, Gaffney BL, Harrison M, Hughes LE, King RA, Krukonis GP, Lopez AJ, Monsen-Collar K, Pizzorno MC, Rinehart CA; SEA-PHAGES Program; PHIRE Program, Staples AK, Stowe EL, Garlena RA, Russell DA, Cresawn SG, Pope WH, Hatfull GF.  Complete Genome Sequences of 44 Arthrobacter Phages. Genome Announc. 2018 Feb 1;6(5). pii: e01474-17. doi: 10.1128/genomeA.01474-17. PubMed PMID: 29437090.  David I. Hanauer, Mark J. Graham, SEA-PHAGES, Laura Betancur, Aiyana Bobrownicki, Steven G. Cresawn, Rebecca A. Garlena, Deborah Jacobs-Sera, Nancy Kaufmann, Welkin H. Pope, Daniel A. Russell, William R. Jacobs, Viknesh Sivanathan, David J. Asai, Graham F. Hatfull*  Inclusive Research Education Community.  Proceedings of the National Academy of Sciences Dec 2017, 201718188; DOI: 10.1073/pnas.1718188115. *CJDaniels contributing author: data collection and program development. Manoj Samanta, Stella Lai, Charles Daniels, Venkat Gopalan Sequence analysis and comparative study of the protein subunits of archaeal RNase P. 2016. Biomolecules. 2016 Apr 20;6(2). pii: E22. doi: 10.3390/biom6020022 Welkin H Pope, Charles A Bowman, Daniel A Russell, Deborah Jacobs-Sera, David J Asai, Steven G Cresawn, William R Jacobs Jr, Roger W Hendrix, Jeffrey G Lawrence, Graham F Hatfull, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education, Mycobacterial Genetics Course.  Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. 2015. eLife 2015;4:e06416. (Sea-Phage Students). Fischer S, John von Freyend S, Sabag-Daigle A, Daniels CJ, Allers T, Marchfelder A. Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii. 2012. Extremophiles. Mar;16(2):333-43.

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. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. 2010. PLoS One. 19;5(3):e9605 (1-20).

Ray, W.C., Ozer, H.G., Armbruster, D.W. Daniels, C.J. 2009 Beyond Identity- When Classical Homology Searching Fails, Why, and What you Can do About It. Bioinformatics, 2009 Ohio Collaborative Conference: 51-56.