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Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

ABSTRACT: Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).

ORGANISM(S): Thermoplasma acidophilum DSM 1728

PROVIDER: GSE21956 | GEO | 2011/09/27

SECONDARY ACCESSION(S): PRJNA126759

REPOSITORIES: GEO

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Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

Project description:Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted). Total RNA of T. acidophilum was isolated with the RNeasy Protect Bacteria Kit (Qiagen). The transcriptomics analysis was performed on TI273075 60mer chips of Roche NimbleGen microarrays (NimbleGen Systems of Iceland, LLC). Probes were selected for all protein sequences (1482) and labelled with Cy3. The median number of probes per sequence is 20, and each probe is replicated 5 times on the chip. The probes are randomly distributed over the surface of the array. Unused features are filled with randomly generated probes of comparable GC content. ArrayStar v2.0 software (DNASTAR, Inc.) was used for the data analysis. Three independent biological replicates were processed for aerobic and anaerobic conditions, respectively.

2011-09-26 | E-GEOD-21956 | biostudies-arrayexpress

Thermoplasma acidophilum DSM 1728

Project description:Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

| PRJNA126759 | ENA

Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus

Project description:This SuperSeries is composed of the following subset Series: GSE28549: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Phenol vs. Benzoate) GSE30798: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Acetate) GSE30799: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Phenol) GSE30801: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Benzoate) Refer to individual Series

2011-07-19 | E-GEOD-30796 | biostudies-arrayexpress

Anaerobic Degradation of Phenylacetate By the Hyperthermophilic Archaeon, Ferroglobus placidus

2014-10-01 | GSE59466 | GEO

Characterization of the DNA gyrase from the thermoacidophilic archaeon Thermoplasma acidophilum.

Project description:Thermoplasma acidophilum is sensitive to the antibiotic drug novobiocin, which inhibits DNA gyrase. We characterized DNA gyrases from T. acidophilum strains in vitro. The DNA gyrase from a novobiocin-resistant strain and an engineered mutant were less sensitive to novobiocin. The novobiocin-resistant gyrase genes might serve as T. acidophilum genetic markers.

| S-EPMC1316996 | biostudies-literature

Anaerobic Degradation of Phenylacetate By the Hyperthermophilic Archaeon, Ferroglobus placidus

Project description:Comparison of acetate- to phenylacetate-grown F. placidus cells to identify genes that are potentially involved in anaerobic phenylacetate degradation by this unique hypertherophilic archaeon. A four chip study using total RNA recovered from two separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM phenylacetate (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition). Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

2014-10-01 | E-GEOD-59466 | biostudies-arrayexpress

Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon.

Project description:Archaeosine (G(+)), which is found only at position 15 in many archaeal tRNA, is formed by two steps, the replacement of the guanine base with preQ0 by archaeosine tRNA-guanine transglycosylase (ArcTGT) and the subsequent modification of preQ0 to G(+) by archaeosine synthase. However, tRNA(Leu) from Thermoplasma acidophilum, a thermo-acidophilic archaeon, exceptionally has two G(+)13 and G(+)15 modifications. In this study, we focused on the biosynthesis mechanism of G(+)13 and G(+)15 modifications in this tRNA(Leu). Purified ArcTGT from Pyrococcus horikoshii, for which the tRNA recognition mechanism and structure were previously characterized, exchanged only the G15 base in a tRNA(Leu) transcript with (14)C-guanine. In contrast, T. acidophilum cell extract exchanged both G13 and G15 bases. Because T. acidophilum ArcTGT could not be expressed as a soluble protein in Escherichia coli, we employed an expression system using another thermophilic archaeon, Thermococcus kodakarensis. The arcTGT gene in T. kodakarensis was disrupted, complemented with the T. acidophilum arcTGT gene, and tRNA(Leu) variants were expressed. Mass spectrometry analysis of purified tRNA(Leu) variants revealed the modifications of G(+)13 and G(+)15 in the wild-type tRNA(Leu). Thus, T. acidophilum ArcTGT has a multisite specificity and is responsible for the formation of both G(+)13 and G(+)15 modifications.

| S-EPMC4770233 | biostudies-literature

Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum.

Project description:Thermoplasma acidophilum is a thermophilic archaeon that uses both non-phosphorylative Entner-Doudoroff (ED) pathway and Embden-Meyerhof-Parnas (EMP) pathway for glucose degradation. While triosephosphate isomerase (TPI), a well-known glycolytic enzyme, is not involved in the ED pathway in T. acidophilum, it has been considered to play an important role in the EMP pathway. Here, we report crystal structures of apo- and glycerol-3-phosphate-bound TPI from T. acidophilum (TaTPI). TaTPI adopts the canonical TIM-barrel fold with eight α-helices and parallel eight β-strands. Although TaTPI shares ~30% sequence identity to other TPIs from thermophilic species that adopt tetrameric conformation for enzymatic activity in their harsh physiological environments, TaTPI exists as a dimer in solution. We confirmed the dimeric conformation of TaTPI by analytical ultracentrifugation and size-exclusion chromatography. Helix 5 as well as helix 4 of thermostable tetrameric TPIs have been known to play crucial roles in oligomerization, forming a hydrophobic interface. However, TaTPI contains unique charged-amino acid residues in the helix 5 and adopts dimer conformation. TaTPI exhibits the apparent Td value of 74.6°C and maintains its overall structure with some changes in the secondary structure contents at extremely acidic conditions (pH 1-2). Based on our structural and biophysical analyses of TaTPI, more compact structure of the protomer with reduced length of loops and certain patches on the surface could account for the robust nature of Thermoplasma acidophilum TPI.

| S-EPMC4692482 | biostudies-literature

Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum.

Project description:Replicative DNA helicases are ring-shaped hexamers that play an essential role in chromosomal DNA replication. They unwind the two strands of the duplex DNA and provide the single-stranded (ss) DNA substrate for the polymerase. The minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in eukarya and archaea. The proteins of only a few archaeal organisms have been studied and revealed that although all have similar amino acid sequences and overall structures they differ in their biochemical properties. In this report the biochemical properties of the MCM protein from the archaeon Thermoplasma acidophilum is described. The enzyme has weak helicase activity on a substrate containing only a 3'-ssDNA overhang region and the protein requires a forked DNA structure for efficient helicase activity. It was also found that the helicase activity is stimulated by one of the two T.acidophilum Cdc6 homologues. This is an interesting observation as it is in sharp contrast to observations made with MCM and Cdc6 homologues from other archaea in which the helicase activity is inhibited when bound to Cdc6.

| S-EPMC1669734 | biostudies-literature

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-03-11 | GSE127727 | GEO

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