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Series GSE10133 Query DataSets for GSE10133
Status Public on Feb 11, 2008
Title Architecture of thermal adaptation in Exiguobacterium sibiricum strain 255-15: A genome and transcriptome approach
Organism Exiguobacterium sibiricum 255-15
Experiment type Expression profiling by array
Summary Several microorganisms have wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments. To better understand thermal adaptation of psychrotrophs, Exiguobacterium sibiricum strain 255-15 was used, a psychrotrophic bacterium that grows from -5°C to 39°C. Its genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 CDS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 10°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response.
Keywords: stress response to cold and hot temperatures
 
Overall design Six-condition experiment: -2.5°C vs10°C, -2.5°C vs 28°C, -2.5°C vs 39°C, 28°C vs10°C, 28°C vs 39°C, 10°C vs 39°C. Biological replicates: 6 replicates grown and harvested independently for each different temperature (-2.5°C, 10°C, 28°C and 39°C). One replicate per array.
 
Contributor(s) Rodrigues DF, Ivannova N, Zhou J, He Z, Huebner M, Tiedje JM
Citation(s) 19019206
Submission date Jan 10, 2008
Last update date Mar 19, 2012
Contact name Debora Frigi Rodrigues
E-mail(s) [email protected]
Fax 517-353-2917
Organization name Michigan State University
Department Microbiology and Molecular Genetics
Lab Center for Microbial Ecology
Street address 540 Plant and Soil Science Bldg.
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Platforms (1)
GPL6358 MSU/JMT Exiguobacterium sibiricum 70mer array v. 1.0
Samples (36)
GSM256115 Comparison 10°C versus 28°C - Replicate 1
GSM256116 Comparison 10°C versus 28°C - Replicate 2
GSM256117 Comparison 10°C versus 28°C - Replicate 3
Relations
BioProject PRJNA108679

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10133_RAW.tar 30.0 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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