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Archaeal postgenomic biology and biotechnology
Research Interests
Our research interests include
broadly the fields of molecular biology, genomics, functional genomics and
biotechnology of halophilic Archaea (haloarchaea). Haloarchaea are excellent
models for fundamental processes, such as DNA replication, transcription and
gene regulation, and translation and for mechanisms of survival in extreme
environments. They are superb experimental organisms, being both easy to
culture and genetically tractable. Over the last 20 years, our research
interests developed along three lines: (1) Analysis of high-frequency gas
vesicle mutants, quite surprisingly, led to the identification of a large gvp gene cluster with over a dozen genes
required for biogenesis of the buoyant organelles. Genetic and immunological
analysis implicated nearly all the gvp
genes in wild-type gas vesicle formation. (2) Analysis of the large replicon
coding for gas vesicles, pNRC100, propelled us into mapping and sequencing the
entire Halobacterium sp. NRC-1
genome. High-throughput sequencing and whole-genome annotation was done with
collaborators at 12 institutions. We hosted the genome jamboree in
Recent efforts have been
directed at advancing Halobacterium
sp. NRC-1 into the forefront of biology as a model system and developing its
biotechnological potential. Our accomplishments include the following: (1) We tested our genetic knockout system for analysis of gene
function and gene regulation in multiple studies. One study focused on arsenic
resistance genes, which led to the discovery of a novel methylase
gene involved in detoxification. (2) We mapped functional replication origins
for the large chromosome and extrachromosomal pNRC replicons. A complex relationship
between members of the large orc-cdc6
family and rep genes and cis-acting
genomic regions were revealed. (3) We developed a custom in situ whole genome oligonucleotide microarray for transcriptome
analysis. The microarray was tested after exposure to a variety of
environmental perturbations. This platform provided excellent design
flexibility and requires minimum labor. (4) We generated a 2-D map of the
proteome of our model. (5) We developed bioinformatics tools and databases for
genome annotation, comparative genomics, and global gene regulation studies
(see our HaloGenome
website).
In addition to our major
research interests, an important professional goal is to contribute to science
education and communication. To advance these goals, we have edited a
laboratory manual on Halophiles, published by Cold Spring Harbor Laboratory
Press and developed a set of set of interactive computer modules for teaching
concepts in molecular genetics, called MOLGENT. We have also initiated a new
set of laboratory kits (“New Model Microbe”)
for teaching fundamental biological concepts using halophiles to high school
and college students, marketed through Carolina Biological Supply Company.
These kits are being used at many institutions (for some examples, see our Outreach projects).
Finally, we have launched a new open access, peer-reviewed, online journal
named Saline Systems, published
by BioMed Central. Papers published in Saline
Systems are full-text archived in PubMed Central.
The goal of the journal is to foster integration, cooperation, and communication
among a diversity of scientists studying the biology of coastal and inland
saline environments and halophilic organisms.
Recent Publications
Berquist, B.R. and S. DasSarma. 2008. DNA replication in Archaea. In Archaea:
new models for prokaryotic biology. Horizon Press, P. Blum (ed.),
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.
DeVeaux, L.C., Müller, J.A.,
Smith, J., Petrisko, J., Wells, D.P., and S.
DasSarma. 2007. Extremely
radiation-resistant mutants of a halophilic archaeon with increased
single-stranded DNA binding protein (RPA) gene expression. Radiation Res.
168:507-514.
Coker, J.A., P. DasSarma, J. 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.
Giaquinto, L., P.M. Curmi, K.S. Siddiqui, A. Poljak, E. DeLong, S. DasSarma, and R. Cavicchioli. 2007. Structure
and function of cold shock proteins in archaea. J Bacteriol. 189:5738-48.
Berquist, B.R., P. DasSarma, and S.
DasSarma. 2007. Essential and
non-essential DNA replication genes in the model haloarchaeon, Halobacterium
sp. NRC-1. BMC Genetics 8:31.
Sowers, K.R., P. H. Blum, and S.
DasSarma. 2007. Genetics of
Archaea. In C.A. Reddy, T.J. Beveridge, J.A.
Breznak, G.A. Marzluf, T.M.
Schmidt, and L. R. Snyder (ed.), Methods for General and Molecular
Microbiology. 3rd edition. American
Society for Microbiology,
DasSarma, S. 2007. Saline systems highlights for 2006.
Saline Systems 3:1.
Berquist, B.R., J.
Soneja, and S. DasSarma. 2005.
Comparative genomic survey of information transfer systems in two diverse
extremely halophilic Archaea, Halobacterium sp. strain NRC-1 and Haloarcula
marismortui. In Adaptation to Life at High Salt Concentrations in Archaea,
Bacterial, and Eukarya, Gunde-Cimerman,
N, A. Oren, and A. Plemenitas (eds.) Springer, Dordrecht,
Netherlands, pp. 148-182.
Shively, J.M., G.C. Cannon, S. Heinhorst,
D.A. Bryant, S. DasSarma, D. Bazylinski, J. Preiss, A. Steinbuchel, R. Docampo, and C. Dahl. 2005. Bacterial Inclusions. Encyclopedia of Life Sciences, Wiley,
DasSarma, S. and P. DasSarma 2005. Halophiles. Encyclopedia of Life Sciences, Wiley,
DasSarma, S. and P. DasSarma 2006. Halophiles. Encyclopedia
of Life Sciences, Wiley,
Berquist, B.R., J.A.
Müller, and S. DasSarma. 2006. Genetic
Systems for halophilic Archaea. In Methods in Microbiolgy, pp. 637-668, A. Oren and F. Rainey (eds.),
Elsevier/Academic Press.
DasSarma, S., B.R. Berquist, J.A.
Coker, P.
DasSarma, J.A. Müller. 2006. Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. Saline
Systems 2:3.
DasSarma,
S., 2006. Saline systems highlights for 2005. Saline
Systems 2:1.
DasSarma, S. 2006. Extreme
halophiles are models for astrobiology. Microbe 1:120-127.
McCready, S., J.A. Müller,
DasSarma, S. 2005. Saline
Systems: A research journal bridging gene systems and ecosystems. Saline
Systems 1:1.
Berquist, B.R., J. Soneja, and S. DasSarma. 2005. Comparative genomic survey of information transfer systems in two diverse extremely
halophilic Archaea, Halobacterium sp.
strain NRC-1 and Haloarcula marismortui. In Adaptation to Life at High Salt
Concentrations in Archaea, Bacterial, and Eukarya, Gunde-Cimerman, N, A. Oren, and A. Plemenitas (eds.)
Springer, Dordrecht, Netherlands, pp. 148-182.
Baxter, B.K., C.D. Litchfield, K.
Sowers, J.D. Griffith, P.A. DasSarma, and S. DasSarma. 2005.Microbial diversity of
Müller, J.A. and S. DasSarma.
2004. Functional genomic analysis of
anaerobic respiration of the archaeon Halobacterium
sp. NRC-1: dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) as
terminal electron acceptors , J. Bacteriol.
187:1659-1667.
Stuart,
E.S., F. Morshed, M. Sremac, and S. DasSarma. 2004. Cassette-based presentation of SIV epitopes with recombinant gas vesicles from halophilic
archaea. J Biotechnol.
114:225-237.
Jellison, R., Y.S. Zadereev, A.G. Degermendzhy, P.A.
DasSarma, S. DasSarma, G. Zambrana, and J.M. Melack. 2004. Conservation
and Management Challenges of Saline Lakes: A Review of Five LakeNet
Experience Briefs, http://www.worldlakes.org/.
Wang, G., S.K. Kennedy, S. Fasiludeen C., Rensing, and S. DasSarma. 2004.
Arsenic Resistance in Halobacterium
sp. NRC-1 Examined Using an Improved Gene Knockout System. J. Bacteriol. 186:3187-3194.
Shukla,
H.D. and S. DasSarma. 2004. Complexity of Gas Vesicle Biogenesis in
Halobacterium sp. Strain NRC-1: Identification of Five New Proteins. J. Bacteriol. 186:3182-3186.
Mizuki, T., M. Kamekura, S. DasSarma, T. Fukushima, R. Usami, Y. Yoshida, and K. Horikoshi. 2004. Ureases of extreme halophiles of the
genus Haloarcula with a unique structure of
gene cluster. Biosci. Biotechnol.
Biochem.
68:397-406.
DasSarma, S.
2004. Genome sequence of an extremely halophilic archaeon, in Microbial Genomes, pp.
383-399, C.M. Fraser, T. Read, and K.E. Nelson (eds.), Humana Press, Inc,
Goo,
Y.A., J. Roach, G. Glusman, N.S. Baliga,
K. Deutsch, M. Pan, S. Kennedy, S.
DasSarma, W.V. Ng, and L. Hood. 2004. Low-pass
sequencing for microbial comparative genomics. BMC Genomics.
5:3-21.
A tribute
to my father, Professor Basudeb
DasSarma.