Haloferax volcanii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA178711 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR610320.fastq.gz | Fastqsanger.gz | |||
| SRR610321.fastq.gz | Fastqsanger.gz | |||
| SRR610322.fastq.gz | Fastqsanger.gz | |||
| SRR610323.fastq.gz | Fastqsanger.gz | |||
| SRR610324.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:In this study the transcriptome of Haloferax volcanii DS70 (Wendoloski D, Ferrer C, Dyall-Smith ML. Microbiology. 2001, 147: 959-64), grown under of a variety of conditions, was mapped using a custom genome-wide tiled array consisting of 25 nt probes spaced in 35 nt windows. H. volcanii is a facultative aerobe capable of growth on simple carbon and nitrogen sources, it is amenable to genetic manipulations and has become a widely used model organism for studies on haloarchaeal physiology and global gene regulation. Of particular interest is the identification of genes encoding enzymes needed for growth on simple carbon and nitrogen sources and how these cells respond to limitations in these key nutrients. To address these questions we have compared the RNA populations of cells undergoing balanced growth in completely defined minimal medium (CDM) with succinate-glycerol, pyruvate or lactate as sole carbon sources with RNA from cells grown in complex rich medium (CX) containing yeast extract and tryptone. Data from these studies have identified a core group of genes expressing during balanced growth in either condition as well as specific genes associated with the biosynthesis of amino acids, nucleotides and other key building blocks. The response to nutrient limitation was also investigated. RNA populations from cells entering stationary phase from growth in CDM and CX media were compared to those undergoing balanced growth, and these RNAs were also compared with RNA populations of cells subjected to nitrogen or carbon starvation. Growth in the presence of histidine as the sole source of nitrogen in CDM medium also presented a model for growth with a “poor” nitrogen source. The results of these studies identified specific subpopulations of genes associated with nitrogen limitation and general nutrient limitation associated with the transition to stationary phase. Many of the responsive protein encoding genes were assigned general functions based on their similarity to known proteins; however, in each comparison, approximately half of the affected genes encode proteins classified as unknown or hypothetical proteins. The haloarchaea are also distinct among the Archaea in having multiple genes encoding the general transcription factor proteins TATA binding protein (TBP) and transcription factor IIB (TFB). We observed differential expression of these genes, providing further support for the proposal that alternative TBP-TFB pairings are associated with programmed changes in gene expression in the haloarchaea. RNA was prepared from H. volcanii DS70 cells grown under a variety of conditions. These include: balanced growth in completely defined medium with succinate and glycerol, pyruvate, or lactate as sole carbon source; balanced growth in complex medium with yeast extract and tryptone; starvation for nitrogen or carbon by re-suspending cells, undergoing balanced growth, in media lacking these agents; balanced growth in the presence of low (10% w/v NaCl) and high (20 % or 25% w/v NaCl) salt, and cells entering stationary from growth in CDM or CX media. Four independent cultures were prepared for each growth variable and RNA was isolated from each culture. RNA samples were identified as acceptable for use in array analysis if clear 23S rRNA, 16S rRNA and tRNA-sized bands were present in agarose gel and capillary electrophoresis analysis of the samples. Three RNA samples were chosen for each growth variable and each was used as the source material for a separate chip experiment; these constituted three biological replicates for the growth variable. Data from 48 chip hybridizations, representing 16 growth conditions, were combined for the quantile scaling (Auer H, Newsom DL, Nowak NJ, McHugh KM, Singh S, Yu CY, Yang Y, Wenger GD, Gastier-Foster JM, Kornacker K. BMC Genomics. 2007, 8:111-124) presented in the data analyses. Two additional experiments are included where the RNAs of three independent biological samples were pooled into a single RNA population and used as the source material for an array experiment. These included RNA samples enriched for species less than 500 nt that were isolated from cells undergoing balanced growing, and entry into stationary phase, in CDM or CX media. A second pooled series were obtained from the H. volcanii DS70 mutant strains ASD40 (∆pyrF) and ASD41 (∆pyrF∆hutR) grown in CDM with ammonium ion or histidine as the sole source of nitrogen. Pooled samples are presented as quantile normalized values (Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. Bioinformatics. 2003, 19: 185-193). Total genomic DNA from H. volcanii DS70 was also used as probe, in two independent array experiments, to measure the inherent hybridization to the probes. These data are presented as quantile scaled values (Auer et. al., 2007).
2010-09-08 | E-GEOD-18066 | biostudies-arrayexpress
Project description:Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. The multi-origin main chromosome has split into two genome elements via homologous recombination. The newly generated elements possess all the features of bona fide chromosomes. To our knowledge, the spontaneous generation of a new chromosome in prokaryotes without horizontal gene transfer has not been reported previously.
2018-04-17 | GSE108201 | GEO
Project description:In this study the transcriptome of Haloferax volcanii DS70 (Wendoloski D, Ferrer C, Dyall-Smith ML. Microbiology. 2001, 147: 959-64), grown under of a variety of conditions, was mapped using a custom genome-wide tiled array consisting of 25 nt probes spaced in 35 nt windows. H. volcanii is a facultative aerobe capable of growth on simple carbon and nitrogen sources, it is amenable to genetic manipulations and has become a widely used model organism for studies on haloarchaeal physiology and global gene regulation. Of particular interest is the identification of genes encoding enzymes needed for growth on simple carbon and nitrogen sources and how these cells respond to limitations in these key nutrients. To address these questions we have compared the RNA populations of cells undergoing balanced growth in completely defined minimal medium (CDM) with succinate-glycerol, pyruvate or lactate as sole carbon sources with RNA from cells grown in complex rich medium (CX) containing yeast extract and tryptone. Data from these studies have identified a core group of genes expressing during balanced growth in either condition as well as specific genes associated with the biosynthesis of amino acids, nucleotides and other key building blocks. The response to nutrient limitation was also investigated. RNA populations from cells entering stationary phase from growth in CDM and CX media were compared to those undergoing balanced growth, and these RNAs were also compared with RNA populations of cells subjected to nitrogen or carbon starvation. Growth in the presence of histidine as the sole source of nitrogen in CDM medium also presented a model for growth with a “poor” nitrogen source. The results of these studies identified specific subpopulations of genes associated with nitrogen limitation and general nutrient limitation associated with the transition to stationary phase. Many of the responsive protein encoding genes were assigned general functions based on their similarity to known proteins; however, in each comparison, approximately half of the affected genes encode proteins classified as unknown or hypothetical proteins. The haloarchaea are also distinct among the Archaea in having multiple genes encoding the general transcription factor proteins TATA binding protein (TBP) and transcription factor IIB (TFB). We observed differential expression of these genes, providing further support for the proposal that alternative TBP-TFB pairings are associated with programmed changes in gene expression in the haloarchaea.
2010-09-08 | GSE18066 | GEO
Project description:The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. We identified TbsP binding sites in the presence and absence of glucose to better understand the role of TbsP. TbsP does not bind DNA in response to glucose availability. The sole binding site near a metabolic enzyme-coding gene is upstream of gapII.
2023-12-01 | GSE248565 | GEO
Project description:Extracellular DNA is found in all environments and is a dynamic component of the microbial ecosystem. Microbial cells produce and interact with extracellular DNA through many endogenous mechanisms. Extracellular DNA is processed and internalized for use as genetic information and as a major source of macronutrients, and plays several key roles within prokaryotic biofilms. Hypersaline sites contain some of the highest extracellular DNA concentrations measured in nature-a potential rich source of carbon, nitrogen, and phosphorus for halophilic microorganisms. We conducted DNA growth studies for the halophilic archaeon Haloferax volcanii DS2 and show that this model Halobacteriales strain is capable of using exogenous double-stranded DNA as a nutrient. Further experiments with varying medium composition, DNA concentration, and DNA types revealed that DNA is utilized primarily as a phosphorus source, that growth on DNA is concentration-dependent, and that DNA isolated from different sources is metabolized selectively, with a bias against highly divergent methylated DNA. Additionally, fluorescence microscopy showed that labeled DNA co-localized with H. volcanii cells. The gene Hvo_1477 was also identified using a comparative genomic approach as a factor likely to be involved in DNA processing at the cell surface, and deletion of Hvo_1477 created a strain deficient in the ability to grow on extracellular DNA. Widespread distribution of Hvo_1477 homologs in archaea suggests metabolism of extracellular DNA may be of broad ecological and physiological relevance in this domain of life.
| S-EPMC3929857 | biostudies-literature
Project description:A cytochrome in an extremely halophilic archaeon, Haloferax volcanii, was purified to homogeneity. This protein displayed a redox difference spectrum that is characteristic of a-type cytochromes and a CN(-) complex spectrum that indicates the presence of heme a and heme a(3). This cytochrome aa(3) consisted of 44- and 35-kDa subunits. The amino acid sequence of the 44-kDa subunit was similar to that of the heme-copper oxidase subunit I, and critical amino acid residues for metal binding, such as histidines, were highly conserved. The reduced cytochrome c partially purified from the bacterial membrane fraction was oxidized by the cytochrome aa(3), providing physiological evidence for electron transfer from cytochrome c to cytochrome aa(3) in archaea.
| S-EPMC139504 | biostudies-literature
Project description:We have comprehensively explored the origin utilisation in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated.
2015-07-08 | GSE70597 | GEO
Project description:We have comprehensively explored the origin utilisation in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated. Genomic DNA was extracted from the H. mediterranei cultures at specific time points(12h,18h,24h,36h,42h and stationary phase 66h), or during the exponential phase (OD600≈0.5) and stationary phase (OD600≈4.0)for the origin deletion strains. After being lablled, Genomic DNA from exponential phase and stationary phase were hybridized to Haloferax mediterranei genome array genechips.
2015-07-08 | E-GEOD-70597 | biostudies-arrayexpress
Project description:Haloferax volcanii, an extreme halophile originally isolated from the Dead Sea, is used worldwide as a model organism for furthering our understanding of archaeal cell physiology. In this study, a combination of approaches was used to identify a total of 1296 proteins, representing 32% of the theoretical proteome of this haloarchaeon. This included separation of (phospho)proteins/peptides by 2-dimensional gel electrophoresis (2-D), immobilized metal affinity chromatography (IMAC), metal oxide affinity chromatography (MOAC), and Multidimensional Protein Identification Technology (MudPIT) including strong cation exchange (SCX) chromatography coupled with reversed phase (RP) HPLC. Proteins were identified by tandem mass spectrometry (MS/MS) using nanoelectrospray ionization hybrid quadrupole time-of-flight (QSTAR XL Hybrid LC/MS/MS System) and quadrupole ion trap (Thermo LCQ Deca). Results indicate that a SCX RP HPLC fractionation coupled with MS/MS provides the best high-throughput workflow for overall protein identification.
| S-EPMC2676566 | biostudies-literature
Project description:To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable-the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this prokaryotic defence system is present in 90% of archaeal and 40% of bacterial species, and enables foreign intruders to be eliminated in a sequence-specific manner. There are three major types (I-III) and at least 14 subtypes of this system, with only some of the subtypes having been analysed in detail, and many aspects of the defence reaction remaining to be elucidated. Few archaeal examples have so far been analysed. Here we summarize the characteristics of the CRISPR-Cas system of Haloferax volcanii, an extremely halophilic archaeon originally isolated from the Dead Sea. It carries a single CRISPR-Cas system of type I-B, with a Cascade like complex composed of Cas proteins Cas5, Cas6b and Cas7. Cas6b is essential for CRISPR RNA (crRNA) maturation but is otherwise not required for the defence reaction. A systematic search revealed that six protospacer adjacent motif (PAM) sequences are recognised by the Haloferax defence system. For successful invader recognition, a non-contiguous seed sequence of 10 base-pairs between the crRNA and the invader is required.
| S-EPMC4390866 | biostudies-literature