H. salinarum R1 wildtype vs cyc-
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ABSTRACT:
ORGANISM(S): Halobacterium salinarum Halobacterium salinarum NRC-1
PROVIDER: GSE104012 | GEO | 2017/09/20
SECONDARY ACCESSION(S): PRJNA407939
REPOSITORIES: GEO
Similar Datasets
Project description:H. salinarum R1 wildtype vs cyc-
| PRJNA407939 | ENA
Project description:To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. Homology searches identified putative RNase genes in H. salinarum NRC-1 that include likely orthologs for RNases found in prokaryotic and eukaryotic lineages. The VNG2099C protein sequence is significantly similar (e = 2 x 10^-34) to the sequence of the rat liver perchloric acid-soluble protein (L-PSP), which has been shown to have endoribonuclease activity in vitro (Morishita et al 1999). The VNG2099C protein, like the archaeal Sulfolobus tokodaii YjgF/L-PSP protein for which a crystal structure has been solved (Miyakawa et al 2006), shares conservation of residues proposed to constitute the active site of the rat protein. The purpose of this gene expression study was to investigate the role of the putative endoribonuclease VNG2099C on gene regulation.
2014-03-03 | GSE45988 | GEO
Project description:Halobacterium salinarum R1, DSM 671 Genome sequencing
| PRJNA298090 | ENA
Project description:To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. Homology searches identified putative RNase genes in H. salinarum NRC-1 that include likely orthologs for RNases found in prokaryotic and eukaryotic lineages. The VNG2099C protein sequence is significantly similar (e = 2 x 10^-34) to the sequence of the rat liver perchloric acid-soluble protein (L-PSP), which has been shown to have endoribonuclease activity in vitro (Morishita et al 1999). The VNG2099C protein, like the archaeal Sulfolobus tokodaii YjgF/L-PSP protein for which a crystal structure has been solved (Miyakawa et al 2006), shares conservation of residues proposed to constitute the active site of the rat protein. The purpose of this gene expression study was toM-BM- investigate the role of the putative endoribonuclease VNG2099C on gene regulation. The relative changes in transcript levels were determined for wild type (Dura3) and the VNG2099C knockout.
2014-03-03 | E-GEOD-45988 | biostudies-arrayexpress
Project description:Medium-adapted cultures of H. salinarum were grown in synthetic medium with or without AroAA, and cells harvested by centrifugation after growth had reached OD600nm=0.2 and 0.58, respectively.
2014-12-01 | E-MEXP-3818 | biostudies-arrayexpress
Project description:BackgroundPhototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea.Methodology/principal findingsWe developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis.Conclusion/significanceThis is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.
| S-EPMC2020435 | biostudies-literature
Project description:Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH-LC/MS/MS. Using a simple surfactant-assisted protein solubilization protocol and one-dimensional ultrahigh performance nanoflow chromatography on the front end, 63.2% and 58.6% of the predicted Hbt. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicate that we achieved a comprehensive characterization of the proteome. 60.8% of quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and biofilm states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Taken together our results and analysis constitute the first comprehensive study to track the molecular changes from planktonic cells to initial and mature archaeal biofilms on the proteome level. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT-PCR to test the feasibility of establishing rapid PCR-based assays for archaeal biofilm formation.
2016-09-28 | PXD003667 | Pride