Gene Expression Regulation, Archaeal
Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data. (1/15)The hyperthermophilic, facultatively heterotrophic crenarchaeum Thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total genome), with an average gap size of 100 bp and 5.3-fold coverage, are reported, giving insights into the genome of T. tenax. Genome analysis and biochemical studies enabled us to reconstruct its central carbohydrate metabolism. T. tenax uses a variant of the reversible Embden-Meyerhof-Parnas (EMP) pathway and two different variants of the Entner-Doudoroff (ED) pathway (a nonphosphorylative variant and a semiphosphorylative variant) for carbohydrate catabolism. For the EMP pathway some new, unexpected enzymes were identified. The semiphosphorylative ED pathway, hitherto supposed to be active only in halophiles, is found in T. tenax. No evidence for a functional pentose phosphate pathway, which is essential for the generation of pentoses and NADPH for anabolic purposes in bacteria and eucarya, is found in T. tenax. Most genes involved in the reversible citric acid cycle were identified, suggesting the presence of a functional oxidative cycle under heterotrophic growth conditions and a reductive cycle for CO2 fixation under autotrophic growth conditions. Almost all genes necessary for glycogen and trehalose metabolism were identified in the T. tenax genome. (+info)
Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. (2/15)A novel virus, termed Pyrobaculum spherical virus (PSV), is described that infects anaerobic hyperthermophilic archaea of the genera Pyrobaculum and Thermoproteus. Spherical enveloped virions, about 100 nm in diameter, contain a major multimeric 33-kDa protein and host-derived lipids. A viral envelope encases a superhelical nucleoprotein core containing linear double-stranded DNA. The PSV infection cycle does not cause lysis of host cells. The viral genome was sequenced and contains 28337 bp. The genome is unique for known archaeal viruses in that none of the genes, including that encoding the major structural protein, show any significant sequence matches to genes in public sequence databases. Exceptionally for an archaeal double-stranded DNA virus, almost all the recognizable genes are located on one DNA strand. The ends of the genome consist of 190-bp inverted repeats that contain multiple copies of short direct repeats. The two DNA strands are probably covalently linked at their termini. On the basis of the unusual morphological and genomic properties of this DNA virus, we propose to assign PSV to a new viral family, the Globuloviridae. (+info)
The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. (3/15)Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner-Doudoroff) pathway generally proceeds via a non-phosphorylative variant. A key enzyme of the non-phosphorylating ED pathway of Sulfolobus solfataricus, KDG (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. In the present study, a comparative genomics analysis is described that reveals conserved ED gene clusters in both Thermoproteus tenax and S. solfataricus. The corresponding ED proteins from both archaea have been expressed in Escherichia coli and their specificity has been identified, revealing: (i) a novel type of gluconate dehydratase (gad gene), (ii) a bifunctional 2-keto-3-deoxy-(6-phospho)-gluconate aldolase (kdgA gene), (iii) a 2-keto-3-deoxygluconate kinase (kdgK gene) and, in S. solfataricus, (iv) a GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; gapN gene). Extensive in vivo and in vitro enzymatic analyses indicate the operation of both the semi-phosphorylative and the non-phosphorylative ED pathway in T. tenax and S. solfataricus. The existence of this branched ED pathway is yet another example of the versatility and flexibility of the central carbohydrate metabolic pathways in the archaeal domain. (+info)
Genes for stable RNA in the extreme thermophile Thermoproteus tenax: introns and transcription signals. (4/15)To investigate gene organization and expression signals in extreme thermophilic archaebacteria, tRNA genes were cloned from Thermoproteus tenax. Clones for five tRNA species were obtained, namely for tRNAAla (TGC), tRNAAla (CGC), tRNALeu (CAG), tRNALeu (CAA) and tRNAMet (CAT). Three of the respective genes were located singly in the chromosome, the two others (tRNAAla and tRNAMet) were clustered but in a head to head position. Four of the genes contained intervening sequences, either in the classical position 3' to the anticodon (tRNAMet), or within the anticodon sequence (tRNALeuCAG), or in the hitherto unique position 5' to the anticodon within the anticodon stem region (tRNAAla). Existence of a transcript containing the intervening sequence was demonstrated by nuclease S1 mapping. All tRNA genes were extremely rich in G-C basepairs of helical regions, a feature which may contribute to thermostability of the secondary structure. The start site of transcription of the 16S/23S rRNA operon and of two tRNA genes of Thermoproteus was determined by nuclease S1 mapping. Transcription of the tRNA genes initiates close to or immediately at the 5' end of the structural gene, that of the rRNA operon 175 bp upstream of the coding region. About 18 bp upstream of the transcription initiation site a conserved AT-rich sequence motif occurs within a fairly GC-rich intercistronic spacer. Its putative instability at the high growth temperature of Thermoproteus suggests a function as entry site for RNA polymerase. (+info)
TTSV1, a new virus-like particle isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. (5/15)A new virus-like particle TTSV1 was isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax sampled at a hot spring region in Indonesia. TTSV1 had a spherical shape with a diameter of approximately 70 nm and was morphologically similar to the PSV isolated from a strain of Pyrobaculum. The 21.6 kb linear double-stranded DNA genome of TTSV1 had 38 open reading frames (ORFs), of which 15 ORFs were most similar to those of PSV. The remaining 23 ORFs showed little similarity to proteins in the public databases. Southern blot analysis demonstrated that the viral genome is not integrated into the host chromosome. TTSV1 consisted of three putative structural proteins of 10, 20, and 35 kDa in size, and the 10-kDa major protein was identified by mass spectrometry as a TTSV1 gene product. TTSV1 could be assigned as a new member of the newly emerged Globuloviridae family that includes so far only one recently characterized virus PSV. (+info)
CC1, a novel crenarchaeal DNA binding protein. (6/15)The genomes of the related crenarchaea Pyrobaculum aerophilum and Thermoproteus tenax lack any obvious gene encoding a single-stranded DNA binding protein (SSB). SSBs are essential for DNA replication, recombination, and repair and are found in all other genomes across the three domains of life. These two archaeal genomes also have only one identifiable gene encoding a chromatin protein (the Alba protein), while most other archaea have at least two different abundant chromatin proteins. We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax. An assay for proteins capable of binding to a single-stranded DNA oligonucleotide resulted in identification of three proteins. The first protein, Alba, has been shown previously to bind single-stranded DNA as well as duplex DNA. The two other proteins, which we designated CC1 (for crenarchaeal chromatin protein 1), are very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes. CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax. This protein binds single- and double-stranded DNAs with similar affinities. These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein. (+info)
Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes. (7/15)BACKGROUND: The presence of the branched Entner-Doudoroff (ED) pathway in two hyperthermophilic Crenarchaea, the anaerobe Thermoproteus tenax and the aerobe Sulfolobus solfataricus, was suggested. However, so far no enzymatic information of the non-phosphorylative ED branch and especially its key enzyme - glycerate kinase - was available. In the T. tenax genome, a gene homolog with similarity to putative hydroxypyruvate reductase/glycerate dehydrogenase and glycerate kinase was identified. RESULTS: The encoding gene was expressed in E. coli in a recombinant form, the gene product purified and the glycerate kinase activity was confirmed by enzymatic studies. The enzyme was active as a monomer and catalyzed the ATP-dependent phosphorylation of D-glycerate forming exclusively 2-phosphoglycerate. The enzyme was specific for glycerate and highest activity was observed with ATP as phosphoryl donor and Mg2+ as divalent cation. ATP could be partially replaced by GTP, CTP, TTP and UTP. The enzyme showed high affinity for D-glycerate (Km 0.02 +/- 0.01 mM, Vmax of 5.05 +/- 0.52 U/mg protein) as well as ATP (Km of 0.03 +/- 0.01 mM, Vmax of 4.41 +/- 0.04 U/mg protein), although at higher glycerate concentrations, substrate inhibition was observed. Furthermore, the enzyme was inhibited by its product ADP via competitive inhibition. Data bank searches revealed that archaeal glycerate kinases are members of the MOFRL (multi-organism fragment with rich leucine) family, and homologs are found in all three domains of life. CONCLUSION: A re-evaluation of available genome sequence information as well as biochemical and phylogenetic studies revealed the presence of the branched ED pathway as common route for sugar degradation in Archaea that utilize the ED pathway. Detailed analyses including phylogenetic studies demonstrate the presence of three distinct glycerate kinase classes in extant organisms that share no common origin. The affiliation of characterized glycerate kinases with the different enzyme classes as well as their physiological/cellular function reveals no association with particular pathways but a separate phylogenetic distribution. This work highlights the diversity and complexity of the central carbohydrate metabolism. The data also support a key function of the conversion of glycerate to 2- or 3-phosphoglycerate via glycerate kinase in funneling various substrates into the common EMP pathway for catabolic and anabolic purposes. (+info)
DNA microarray analysis of central carbohydrate metabolism: glycolytic/gluconeogenic carbon switch in the hyperthermophilic crenarchaeum Thermoproteus tenax. (8/15)(+info)
"Thermoproteus" is not a medical term, but rather a genus name in the field of biology. It refers to a type of archaea, which are single-celled microorganisms that lack a nucleus and other membrane-bound organelles. Thermoproteus species are extremophiles, meaning they thrive in environments with extreme conditions that are hostile to most life forms. Specifically, Thermoproteus species are hyperthermophiles, as they can grow at temperatures up to 105°C (221°F). They are commonly found in volcanic vents and other hydrothermal systems.
While not directly related to medical science, understanding the biology of extremophiles like Thermoproteus can provide insights into the limits of life and the adaptations that allow organisms to survive under extreme conditions. This knowledge can have implications for fields such as astrobiology and the search for extraterrestrial life.
Thermoproteaceae is a family of archaea, a group of single-celled microorganisms that lack a nucleus and are distinct from bacteria and eukaryotes. Thermoproteaceae are part of the order Thermoproteales and belong to the phylum Crenarchaeota. These organisms are extremophiles, meaning they thrive in extreme environments. Specifically, Thermoproteaceae are thermophilic, which means they prefer high temperatures, typically growing optimally between 80-105°C (176-221°F). They are also anaerobic, requiring the absence of oxygen for growth. Some members of this family can also use sulfur compounds as an energy source through a process called sulfur respiration. The cells of Thermoproteaceae are typically rod-shaped or filamentous and may form loose aggregates or mats in their environments.
Thermoproteales is an order of archaea belonging to the class Thermoprotei, within the phylum Crenarchaeota. These are extremophilic organisms, meaning they thrive in extreme environments that are hostile to most life forms. Specifically, Thermoproteales are thermophiles, capable of growing at relatively high temperatures, typically between 75-105 degrees Celsius (167-221 degrees Fahrenheit). They are primarily found in volcanic habitats such as hot springs and deep-sea hydrothermal vents.
Members of Thermoproteales have a unique method of energy production, using sulfur compounds and hydrogen gas as their primary energy sources through a process called sulfur respiration or chemolithotrophy. This sets them apart from other archaea and most bacteria, which typically use organic compounds for energy.
The cells of Thermoproteales are usually rod-shaped and may be either motile with flagella or non-motile. They have a unique cell wall structure that does not contain peptidoglycan, a common component in bacterial cell walls. Instead, their cell walls consist mainly of proteins and polysaccharides.
It is important to note that while I strive to provide accurate information, medical definitions can be complex and ever-evolving. Therefore, for the most up-to-date and comprehensive understanding, it's always best to consult authoritative resources or speak with a healthcare professional.
Gene expression regulation in archaea refers to the complex cellular processes that control the transcription and translation of genes into functional proteins. This regulation is crucial for the survival and adaptation of archaea to various environmental conditions.
Archaea, like bacteria and eukaryotes, use a variety of mechanisms to regulate gene expression, including:
1. Transcriptional regulation: This involves controlling the initiation, elongation, and termination of transcription by RNA polymerase. Archaea have a unique transcription machinery that is more similar to eukaryotic RNA polymerases than bacterial ones. Transcriptional regulators, such as activators and repressors, bind to specific DNA sequences near the promoter region to modulate transcription.
2. Post-transcriptional regulation: This includes processes like RNA processing, modification, and degradation that affect mRNA stability and translation efficiency. Archaea have a variety of RNA-binding proteins and small non-coding RNAs (sRNAs) that play crucial roles in post-transcriptional regulation.
3. Translational regulation: This involves controlling the initiation, elongation, and termination of translation by ribosomes. Archaea use a unique set of translation initiation factors and tRNA modifications to regulate protein synthesis.
4. Post-translational regulation: This includes processes like protein folding, modification, and degradation that affect protein stability and function. Archaea have various chaperones, proteases, and modifying enzymes that participate in post-translational regulation.
Overall, gene expression regulation in archaea is a highly dynamic and coordinated process involving multiple layers of control to ensure proper gene expression under changing environmental conditions.
"Pyrobaculum" is a genus of extremely thermophilic bacteria that can grow at temperatures up to 105 degrees Celsius. The name "Pyrobaculum" comes from the Greek words "pyr" meaning fire and "bakulos" meaning staff, which refers to the rod-shaped structure of these bacteria. These organisms are typically found in hot springs and other extreme environments. They are obligate anaerobes, which means they cannot grow in the presence of oxygen. Pyrobaculum species are also chemolithoautotrophs, which means they obtain energy by oxidizing inorganic compounds and use carbon dioxide as their carbon source for growth. It is important to note that "Pyrobaculum" is a scientific name used to classify and describe a group of related bacteria, and it is not a medical term or condition.
Archaea are a domain of single-celled microorganisms that lack membrane-bound nuclei and other organelles. They are characterized by the unique structure of their cell walls, membranes, and ribosomes. Archaea were originally classified as bacteria, but they differ from bacteria in several key ways, including their genetic material and metabolic processes.
Archaea can be found in a wide range of environments, including some of the most extreme habitats on Earth, such as hot springs, deep-sea vents, and highly saline lakes. Some species of Archaea are able to survive in the absence of oxygen, while others require oxygen to live.
Archaea play important roles in global nutrient cycles, including the nitrogen cycle and the carbon cycle. They are also being studied for their potential role in industrial processes, such as the production of biofuels and the treatment of wastewater.
Archaeal proteins are proteins that are encoded by the genes found in archaea, a domain of single-celled microorganisms. These proteins are crucial for various cellular functions and structures in archaea, which are adapted to survive in extreme environments such as high temperatures, high salt concentrations, and low pH levels.
Archaeal proteins share similarities with both bacterial and eukaryotic proteins, but they also have unique features that distinguish them from each other. For example, many archaeal proteins contain unusual amino acids or modifications that are not commonly found in other organisms. Additionally, the three-dimensional structures of some archaeal proteins are distinct from their bacterial and eukaryotic counterparts.
Studying archaeal proteins is important for understanding the biology of these unique organisms and for gaining insights into the evolution of life on Earth. Furthermore, because some archaea can survive in extreme environments, their proteins may have properties that make them useful in industrial and medical applications.
Phylogeny is the evolutionary history and relationship among biological entities, such as species or genes, based on their shared characteristics. In other words, it refers to the branching pattern of evolution that shows how various organisms have descended from a common ancestor over time. Phylogenetic analysis involves constructing a tree-like diagram called a phylogenetic tree, which depicts the inferred evolutionary relationships among organisms or genes based on molecular sequence data or other types of characters. This information is crucial for understanding the diversity and distribution of life on Earth, as well as for studying the emergence and spread of diseases.
List of sequenced archaeal genomes
List of bacterial genera named after mythological figures
List of Archaea genera
List of MeSH codes (B07)
Thermoproteus - Wikipedia
Search results | TU Delft Repositories
CDD Conserved Protein Domain Family: SfsA-like
Pre GI: Gene
NRDR - The Non-coding RNA Databases Resource
Tristromaviridae ~ ViralZone
V. Functions of S-layers | TNO Publications
CHEMICAL SEMISYNTHESIS OF APROTININ HOMOLOGS AND DERIVATIVES MUTATED IN P' POSITIONS
CAZy - GH77
Morphological adaptations facilitating attachment for archaeal viruses
Pesquisa | Biblioteca Virtual em Saúde - BRASIL
Phosphofructokinases from extremely thermophilic microorganisms (detailed view)
Pars 2195(thiT) Score=4.4 Pos=-33 [Pyrobaculum arsenaticum DSM 13514
DeCS 2004 - Novos termos
DeCS 2004 - Nuevos términos
DeCS 2004 - Nuevos términos
DeCS 2004 - Nuevos términos
DeCS 2004 - New terms
DeCS 2004 - Novos termos
DeCS 2004 - Novos termos
DeCS 2004 - New terms
DeCS 2004 - Nuevos términos
DeCS 2004 - New terms
DeCS 2004 - Nuevos términos
- The Thermoproteus tenax genome has been completely sequenced. (wikipedia.org)
- Thermoproteus tenax) and nucleation factors for finegrain mineral development (e.g. (tno.nl)
- On the hypothetical protein F154 of the TTV1 virus from Thermoproteus tenax. (uni-bielefeld.de)
- Sequence analysis and a phylogenetic comparison suggest that the Dictyoglomus PPᵢ-PFK represents an ancient lineage and is closely related to those PPᵢPFKѕ from the archaeal Thermoproteus tenax, bacterial Mycobacterium tuberculosis and Amycolatopsis methanolica, and the ATP-PFK from Streptomyces coelicolor, all of which belong to group III PFKѕ. (waikato.ac.nz)
- Thermoproteus neutrophilus V24Sta chromosome, complete genome. (weizmann.ac.il)
- Like other hyperthermophiles, Thermoproteus represents a living example of some of Earth's earliest organisms, located at the base of the Archaea. (wikipedia.org)
- Like all archaea, Thermoproteus possesses unique membrane lipids, which are ether-linked glycerol derivatives of 20 or 40 carbon branched lipids. (wikipedia.org)
- The isolation of a new archaeal virus, Thermoproteus Piliferous Virus 1 (TSPV1), is also presented here. (montana.edu)
- Thermoproteus is a genus of archaeans in the family Thermoproteaceae. (wikipedia.org)