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Series GSE24882 Query DataSets for GSE24882
Status Public on Oct 28, 2010
Title Gene expression under low O2 in Synechocystis sp. PCC 6803 wild type and hik31 mutant
Organism Synechocystis sp. PCC 6803
Experiment type Expression profiling by array
Summary We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O2 concentration (bubbled with 99.9% N2/0.1% CO2). Significant transcriptional changes upon low O2 incubation included up-regulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31. This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and on plasmid pSYSX. We used a knockout mutant lacking the chromosomal copy of hik31 and studied differential transcription during the aerobic- low O2 transition in this ΔHik31 strain and the wild type. We observed two distinct responses to this transition, one Hik31 dependent, the other Hik31 independent. The Hik31 independent responses included the psbA1 induction and genes involved in chlorophyll biosynthesis. In addition, there were changes in a number of genes that may be in involved in assembling or stabilizing Photosystem II (PSII), and the hox operon and the LexA-like protein (Sll1626) were up-regulated during low O2 growth. This family of responses mostly focused on PSII and overall redox control. There was also a large set of genes that responded differently in the absence of the chromosomal Hik31. In the vast majority of these cases, Hik31 functioned as a repressor and transcription was enhanced when Hik31 was deleted. Genes in this category encoded both core and peripheral proteins for Photosystem I and PS II, the main phycobilisome proteins, chaperones, the ATP synthase cluster and virtually all of the ribosomal proteins. These findings, coupled with the fact that ΔHik31 grew better than the wild-type under low O2 conditions, suggested that Hik31 helped to regulate growth and overall cellular homeostasis. We detected changes in the transcription of other regulatory genes that may compensate for the loss of Hik31. We conclude that Hik31 regulates an important series of genes that relate to energy production and growth and that helps to determine how Synechocystis responds to changes in O2 conditions.
Overall design The microarray experiment involved a loop design that compared the wild type and the ΔHik31 strain under aerobic conditions and 1 h following a transition to low oxygen by using an ANOVA model. RNA was extracted from three biological replicates of both the wild type and the ΔHik31 mutant. The three replicates of each strain were grown in a photobioreactor with air bubbling and then bubbled with a 99.9% nitrogen/0.1% carbon dioxide mix. Cells were harvested for RNA extraction at t0, prior to bubbling with nitrogen/carbon dioxide and at t1 after 1 h of nitrogen/carbon dioxide bubbling.
Citation(s) 20929957
Submission date Oct 21, 2010
Last update date Mar 22, 2012
Contact name Tina Summerfield
Phone +64 3 4797578
Fax +64 3 479 7853
Organization name University of Otago
Department Botany
Street address 464 Great King Street
City Dunedin
ZIP/Postal code 9014
Country New Zealand
Platforms (1)
GPL11088 Synechocystis sp. strain PCC 6803 12K full genome array version 4
Samples (12)
GSM611733 Synechocystis sp. PCC 6803_wild type_aerobic_rep1
GSM611952 Synechocystis sp. PCC 6803_wild type_aerobic_t0_rep2
GSM611953 Synechocystis sp. PCC 6803_wild type_aerobic_rep3
BioProject PRJNA132025

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Supplementary file Size Download File type/resource
GSE24882_RAW.tar 6.7 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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