Ph.D. (Microbial Biochemistry), 2004, The Pennsylvania State University

Research Description
My laboratory’s research interests include the biochemistry, genetics, and molecular biology of extremophilic Archaea, focusing on the halophilic (salt loving) members of this Domain of Life. Currently we are pursuing, but not limited to, the following areas of investigation:

Gene Regulation: The eukaryotic transcription system is immensely complex, multifaceted, and difficult to study. However, the simplified mechanism of transcription found in archaeal cells fills the need for a model system that is simple enough to allow us to study this intricate mechanism in vivo and thereby gain a better understanding of transcription in higher eukaryotes.

We are currently employing the transcription system of the haloarchaeon Halobacterium sp. NRC-1 to gain a deeper insight into how archaeal cells use a simplified eukaryotic system to regulate gene expression. The genome sequence of this organism was completed in 2000 and one of the more interesting findings was the presence of multiple copies of homologs of the eukaryotic TFIIB and TBP genes (referred to as TFB and TBP, respectively, in the Archaea). Since pairs of basal transcription factors have been shown to regulate transcription in eukaryotic cells we hypothesized that a similar process was occurring in the Archaea. Halobacterium sp. NRC-1 contains six TBPs and seven TFBs making for a possible 42 combinatorial pairs to regulate transcription.

On-going projects include probing the interactions required to form the TBP-TFB-DNA ternary complex using biochemical, genetic, and transcriptomic approaches.

Stress Response: halophilic Archaea grow optimally in environments with salinities greater than 20% (w/v). Hypersaline environments can be exceptionally dynamic with respect to salinity, pH, temperature, pressure, nutrients, light, and oxygen and therefore should have evolved a method of rapid response to the flux in their environment. We are interested in studying the effects of salinity and temperature on halophilic archaea. In the lab we are focusing on changes in genome-wide expression in the model organisms Halobacterium sp. NRC-1 and Halorubrum lacusprofundi. We are also beginning field experiments to understand if similar processes occur in these organisms’ native habitats.

On-going projects include using biochemical, bioinformatic, genetic, and transcriptomic approaches to map gene regulatory networks to construct the pathways involved in responding to different environmental stresses. The results obtained from these studies will help ascertain how the haloarchaea respond to their changing environment and what genetic pathways are involved in the response.

Recent Publications

DasSarma, S., J. A. Coker, and P. DasSarma. 2010. Archaea. In Desk Encyclopedia of Microbiology, vol. 2. Academic Press.

Slonczewski, J. L., J. A. Coker, and S. DasSarma. 2009. The Microbial Habitability Zone: Surviving with multiple stressors. Microbe. (Invited article)

DasSarma, P., J. A. Coker, V. Huse, and S. DasSarma. 2009. Microorganisms, halophiles, industrial applications. In Encyclopedia of Industrial Biotechnology. Elsevier.

Coker, J. A., P. DasSarma, M. Capes, T. Wallace, K. McGarity, R. Gessler, J. Liu, H. Xiang, B. R. Berquist, S. DasSarma. 2009. Multiple replication origins of Halobacterium sp. NRC-1: Properties of the conserved orc7-dependent oriC1. J. Bacteriol. 191:5253-5261. (reviewed in Faculty of 1000)

DasSarma, S., J. A. Coker, and P. DasSarma. 2008. Archaea. In Encyclopedia of Microbiology, vol. 2. Academic Press.

Ng, W.V., B.R. Berquist, J.A. Coker, M. Capes, T.H. Wu, P. DasSarma, and S. DasSarma. 2008. Genome sequences of Halobacterium salinarum. Genomics 91:548-552.

Lu, Q., J. Han, L. Zhou, J. A. Coker, P. DasSarma, S. DasSarma, and H. Xiang. 2008. Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation. Nucleic Acids Res 36:3031-3042.

Coker, J. A., and S. DasSarma. 2007. Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA. BMC Genetics 8:61.

Coker, J. A., P. DasSarma, J. S. Kumar, J. A. Müller, and S. DasSarma. 2007. Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature. Saline Systems 3:6.

Reid, I. N., W. B. Sparks, S. Lubow, M. McGrath, M. Livio, J. Valenti, K. R. Sowers, H. D. Shukla, S. MacAuley, T. Miller, R. Suvanasuthi, R. Belas, A. Colman, F. T. Robb, P. DasSarma, J. A. Müller, J. A. Coker, R. Cavicchioli, F. Chen, and S. DasSarma. 2006. Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures. International Journal of Astrobiology 5:89-97.

DasSarma, S., B. R. Berquist, J. A. Coker, P. DasSarma, and J. A. Müller. 2006. Postgenomics of the model haloarchaeon Halobacterium sp. NRC-1. Saline Systems 2:3. (Highly Accessed)

Coker, J. A., and J. E. Brenchley. 2006. Protein engineering of a cold-active -galactosidase from Arthrobacter sp. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity. Extremophiles 10:515-24.

Coker, J. A., P. P. Sheridan, J. Loveland-Curtze, K. R. Gutshall, A. J. Auman, and J. E. Brenchley. 2003. Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic Arthrobacter isolate. J Bacteriol 185:5473-82.

Al-Khaldi, S. F., J. Coker, J. R. Shen, and R. L. Burnap. 2000. Characterization of site-directed mutants in manganese-stabilizing protein (MSP) of Synechocystis sp. PCC6803 unable to grow photoautotrophically in the absence of cytochrome c-550. Plant Mol Biol 43:33-41.