Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Change in gene expression in Chlamydomonas reinhardtii upon heat shock

ABSTRACT: This was an accompanying experiment. Previously, the expression of genes hsp70A and hsp70B had been established as being tetrapyrrole-dependent (Kropat et al., 1997, 2000). Since both are well-known heat-shock proteins, we performed a one-step heat shock treatment by shifting the temperatures from 23M-BM-0C to 42M-BM-0C for 45 min. Moreover, this experiment served as an additional global control to further test the reliability of the microarray and our general conditions since the heat shock response in general is quite well investigated. 3988 responding genes were identified. Among them are 22 genes known to be regulated by HS, selected examples are: the heat shock proteins 22A, 22B and 22C, here leading the list of top-regulated genes on place 1 with a FC of 91297 (22A), place 3 with a FC of 45023 (22B) and place 5 with a FC of 6570 (22C). Other examples are several DnaJ-like proteins or the ClpB chaperone, from the Hsp100 family. In total the analysis comprises 8 samples. For heat shock, a 20 ml culture with ~4 M-CM-^W 106 cells per ml in a 100 ml Erlenmeyer flask was incubated at 42M-BM-0C for 45 min in the light with shaking. Control cultures were incubated in the light at 23M-BM-0C (von Gromoff et al., 1989; Kropat et al., 2000). For harvest, cultures were chilled immediately by pouring them onto crushed ice, centrifuged (5 min, 3000 g, 4M-BM-0C) and resuspended in 1 ml TAP. This procedure was repeated three times, resulting in 3 biological replicates.

ORGANISM(S): Chlamydomonas reinhardtii

SUBMITTER: Bjoern Voss

PROVIDER: E-GEOD-20859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii.

Voss Björn B Meinecke Linda L Kurz Thorsten T Al-Babili Salim S Beck Christoph F CF Hess Wolfgang R WR

Plant physiology 20101209 2

Retrograde signaling is a pathway of communication from mitochondria and plastids to the nucleus in the context of cell differentiation, development, and stress response. In Chlamydomonas reinhardtii, the tetrapyrroles magnesium-protoporphyrin IX and heme are only synthesized within the chloroplast, and they have been implicated in the retrograde control of nuclear gene expression in this unicellular green alga. Feeding the two tetrapyrroles to Chlamydomonas cultures was previously shown to tran ...[more]

PMID: 21148414

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Project description:Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation. mRNA of nine independent cultures of wild type strain Rhizobium etli CE3 were sequenced using Illumina GAIIx. Our parameters were: all cultures were taken from exponential phase, at 30M-BM-0C for 30min in control condition; 42M-BM-0C for 30min for the culture subject to heat -shock, and 30min at 30M-BM-0C in supplementary PY medium with 80mM NaCl for the saline shock condition.

Dataset Information

Change in gene expression in Chlamydomonas reinhardtii upon heat shock

Publications

Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii.

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