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Series GSE79420 Query DataSets for GSE79420
Status Public on Mar 24, 2016
Title Genetic Manipulation of Putrescine Biosynthesis Reprograms the Cellular Transcriptome and the Metabolome
Platform organisms Populus trichocarpa x Populus deltoides; Populus euphratica; Populus tremula x Populus alba
Sample organism Populus maximowiczii x Populus nigra
Experiment type Expression profiling by array
Summary Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098]
The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine→putrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels).
 
Overall design 12 two-channel arrays directly comparing RNA from control and high putrescine producing (HP) cell lines of Populus nigra x maximowiczii at 3 and 5 days of growth. Three independent biological replicates derived from cells grown in three independent replicate cultures were used. In addition, each sample and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each).

Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array; barcode ID for each array is indicated in the sample title and raw data file names) but two idependent raw data files were generated from each slide (one for Cy3, the other for Cy5) and processed as though they are single channel (Cy3 and Cy5 signals are calculated and provided for each sample record). Therfore, each sample record is represented as single channel sample.
 
Contributor(s) Page AF, Cseke LJ, Minocha R, Turlapati S, Podila GK, Ulanov A, Li Z, Minocha SC
Citation(s) 27188293
Submission date Mar 21, 2016
Last update date Jun 27, 2016
Contact name Leland J. Cseke
E-mail(s) csekel@uah.edu
Phone 256 824-6774
Organization name The University of Alabama Huntsville
Department Biological Sciences
Lab Cseke Lab
Street address 301 Sparkman Dr.
City Huntsville
State/province AL
ZIP/Postal code 35899
Country USA
 
Platforms (1)
GPL8473 PICME Poplar 28K Series 3
Samples (24)
GSM2097527 Control_day5_rep1_Cy3 [13210254]
GSM2097528 HP_day5_rep1_Cy5 [13210254]
GSM2097529 Control_day5_rep1_Cy5 [13210255]
Relations
BioProject PRJNA316127

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
GSE79420_RAW.tar 65.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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