Academic literature on the topic 'Sulfolobales'

Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarboxylate/4-hydroxybutyrate cycle using oxygen-sensitive pyruvate synthase and phosphoenolpyruvate carboxylase as carboxylating enzymes has been found in members of the anaerobic Desulfurococcales and Thermoproteales. However, Sulfolobales include anaerobic and Desulfurococcales aerobic autotrophic representatives, raising the question of which of the two cycles they use. We studied the mechanisms of autotrophic CO2 fixation in the strictly anaerobic Stygiolobus azoricus (Sulfolobales) and in the facultatively aerobic Pyrolobus fumarii (Desulfurococcales). The activities of all enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were found in the anaerobic S. azoricus. In contrast, the aerobic or denitrifying P. fumarii possesses all enzyme activities of the dicarboxylate/4-hydroxybutyrate cycle. We conclude that autotrophic Crenarchaeota use one of the two cycles, and that their distribution correlates with the 16S rRNA-based phylogeny of this group, rather than with the aerobic or anaerobic lifestyle.

ABSTRACT The crenarchaeal order Sulfolobales collectively contain at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. While specific respiratory complexes in certain Sulfolobales have been characterized previously as proton pumps for maintaining intracellular pH and generating proton motive force, their contribution to sulfur and iron biooxidation has not been considered. For M. sedula growing in the presence of ferrous iron and reduced inorganic sulfur compounds (RISCs), global transcriptional analysis was used to track the response of specific genes associated with these complexes, as well as other known and putative respiratory electron transport chain elements. Open reading frames from all five terminal oxidase or bc 1-like complexes were stimulated on one or more conditions tested. Components of the fox (Msed0467 to Msed0489) and soxNL-cbsABA (Msed0500 to Msed0505) terminal/quinol oxidase clusters were triggered by ferrous iron, while the soxABCDD′ terminal oxidase cluster (Msed0285 to Msed0291) were induced by tetrathionate and S0. Chemolithotrophic electron transport elements, including a putative tetrathionate hydrolase (Msed0804), a novel polysulfide/sulfur/dimethyl sulfoxide reductase-like complex (Msed0812 to Msed0818), and a novel heterodisulfide reductase-like complex (Msed1542 to Msed1550), were also stimulated by RISCs. Furthermore, several hypothetical proteins were found to have strong responses to ferrous iron or RISCs, suggesting additional candidates in iron or sulfur oxidation-related pathways. From this analysis, a comprehensive model for electron transport in M. sedula could be proposed as the basis for examining specific details of iron and sulfur oxidation in this bioleaching archaeon.

CRISPR (cluster of regularly interspaced palindromic repeats)/Cas and CRISPR/Cmr systems of Sulfolobus, targeting DNA and RNA respectively of invading viruses or plasmids are complex and diverse. We address their classification and functional diversity, and the wide sequence diversity of RAMP (repeat-associated mysterious protein)-motif containing proteins encoded in Cmr modules. Factors influencing maintenance of partially impaired CRISPR-based systems are discussed. The capacity for whole CRISPR transcripts to be generated despite the uptake of transcription signals within spacer sequences is considered. Targeting of protospacer regions of invading elements by Cas protein–crRNA (CRISPR RNA) complexes exhibit relatively low sequence stringency, but the integrity of protospacer-associated motifs appears to be important. Different mechanisms for circumventing or inactivating the immune systems are presented.

In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.

Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L−1, (2) Pond-B: 66°C and 2248 mg L−1, (3) Pond-C: 88°C and 198 mg L−1, and (4) Pond-D: 67°C and 340 mg L−1. In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.

ABSTRACT A 3-hydroxypropionate/4-hydroxybutyrate cycle operates in autotrophic CO2 fixation in various Crenarchaea, as studied in some detail in Metallosphaera sedula. This cycle and the autotrophic 3-hydroxypropionate cycle in Chloroflexus aurantiacus have in common the conversion of acetyl-coenzyme A (CoA) and two bicarbonates via 3-hydroxypropionate to succinyl-CoA. Both cycles require the reductive conversion of 3-hydroxypropionate to propionyl-CoA. In M. sedula the reaction sequence is catalyzed by three enzymes. The first enzyme, 3-hydroxypropionyl-CoA synthetase, catalyzes the CoA- and MgATP-dependent formation of 3-hydroxypropionyl-CoA. The next two enzymes were purified from M. sedula or Sulfolobus tokodaii and studied. 3-Hydroxypropionyl-CoA dehydratase, a member of the enoyl-CoA hydratase family, eliminates water from 3-hydroxypropionyl-CoA to form acryloyl-CoA. Acryloyl-CoA reductase, a member of the zinc-containing alcohol dehydrogenase family, reduces acryloyl-CoA with NADPH to propionyl-CoA. Genes highly similar to the Metallosphaera CoA synthetase, dehydratase, and reductase genes were found in autotrophic members of the Sulfolobales. The encoded enzymes are only distantly related to the respective three enzyme domains of propionyl-CoA synthase from C. aurantiacus, where this trifunctional enzyme catalyzes all three reactions. This indicates that the autotrophic carbon fixation cycles in Chloroflexus and in the Sulfolobales evolved independently and that different genes/enzymes have been recruited in the two lineages that catalyze the same kinds of reactions.

Chez les Archaea, tous les processus informationnels, transcription incluse, sont effectués par des protéines proches de celles des Eukarya. Alors que la machinerie transcriptionnelle des archées a été bien caractérisée structurellement et fonctionnellement, très peu d'informations sont disponibles sur la régulation de son activité. En travaillant à la fois avec des modèles cellulaires (crénarchée hyperthermophile Sulfolobus islandicus) et viraux, nous avons pu réaliser une étude approfondie de trois régulateurs transcriptionnels et mieux comprendre les mécanismes de régulation transcriptionnelle chez les archées. Au cours de cette thèse, deux régulateurs viraux, SvtR et AFV1p06, et un régulateur cellulaire, Sta1, ont été étudiés. Concernant SvtR, codé par le virus SIRV1 qui infecte S. islandicus, nous avons poursuivi la recherche précédente, qui avait permis de déterminer sa structure et sa fonction, en nous focalisant sur la caractérisation de l'ensemble de ses cibles dans le génome viral et sur l'étude de son mécanisme d'action. Pour cela, la séquence du site consensus reconnu par SvtR a été établie à l'aide de la mutagénèse systématique d'un de ses sites déjà caractérisés. Ce site est présent dans les promoteurs de dix gènes de SIRV1 montrant que SvtR pourrait réguler l'activité de plus de 20% des gènes viraux. Ses cibles incluent tous les gènes codant pour les protéines de la capside virale. L'analyse fonctionnelle réalisée sur une partie des sites de liaison de SvtR a permis de démontrer qu'il s'agit d'un régulateur polyvalent agissant, selon la cible, en tant que activateur ou répresseur transcriptionnel. En prenant comme modèle le promoteur du gène gp30, nous avons pu démontrer par plusieurs approches que la régulation de ce promoteur inclut la polymérisation de la protéine depuis son site de liaison principal jusqu’à la TATA-box du promoteur. Il s’agit d’un mécanisme de régulation de transcription à distance original et inédit chez les archées. La structure de l’autre régulateur viral étudié, AFV1p06, codé par le virus AFV1 qui infecte Acidianus hospitalis, révèle la présence au sein de cette protéine d’un domaine en doigt de zinc C2H2, considéré jusqu’à présent comme spécifique des eucaryotes. Nous avons démontré la capacité d’AFV1p06 à se lier à l’ADN avec une préférence pour les régions riches en GC. AFV1p06 est la première DNA binding protéine d’archées de ce type caractérisée in vitro. Le troisième régulateur transcriptionnel, Sta1, est codé par le génome des Sulfolobales. Il est capable d’activer la transcription de gènes viraux, ainsi que du gène chromosomique radA en réponse à un dommage à l’ADN. Pour comprendre son rôle dans la cellule, nous avons tenté de réaliser, sans succès, un mutant knock-out du gène sta1 de S. islandicus RYE15A, ce qui indique que le gène sta1 serait un gène essentiel. L’étude de l’interaction hôte-virus sur le modèle S. islandicus LAL14/1 est un des sujets principaux de notre laboratoire. Le séquençage du génome de cette souche a ouvert la voie pour établir un système génétique. Plusieurs mutants KO de LAL14/1 (pyrEF-; ΔCRISPR1) ont été construits. L’impossibilité d’inactiver un autre gène candidat, topR2, codant pour une réverse gyrase, indique qu’il s’agit d’un gène essentiel. La construction du mutant ΔCRISPR1 est la première étape pour obtenir un dérivé de LAL14/1 dépourvu de système CRISPR, un mutant très utile pour mieux comprendre l’implication des CRISPRs dans le phénotype de résistance de LA14/1 au virus SIRV1 et leur rôle chez les archées en général. L’ensemble des résultats de cette thèse contribue à la meilleure compréhension du fonctionnement moléculaire chez les archées et leurs virus
In Archaea cells all information processes, including transcription, are performed by the Eukarya-like proteins. While the transcriptional machinery of archaea has been well characterized structurally and functionally, very few information concerning the regulation of its activity is available. By working with both cell (crenarchaeota Sulfolobus islandicus) and viral models, we have performed an in-depth study of three transcriptional regulators: two viral regulators, SvtR and AFV1p06, and a cell regulator Sta1. The obtained results allow to better understand the mechanisms of transcriptional regulation in archaea. Concerning the protein SvtR encoded by the virus SIRV1 that infects S. islandicus, we continued the research project that had identified its structure and function. We were focused on identification and characterization of all of SvtR targets in the viral genome and on the study of the mechanisms of regulation. For this purpose, we established the sequence of consensus site recognized by SvtR using systematic mutagenesis of one of its previously characterized binding sites. This site is present in the promoters of 10 genes meaning that SvtR may regulate the activity of more than 20% of SIRV1 genes. Its targets include all known genes encoding proteins of the viral capsid. Functional analysis of SvtR has demonstrated that, according to the target, this protein is a versatile regulator acting as transcriptional activator or repressor. Taking as a model the gp30 gene promoter, we demonstrated by several approaches that regulation of this promoter includes the polymerization of the protein from its primary binding site towards the TATA-box. Such a mechanism of transcriptional regulation is new in archaea. Second, we performed a structural analysis of the protein AFV1p06 encoded by the virus AFV1 which infects Acidianus hospitalis. The structural analysis of AFV1p06 revealed the presence of a C2H2 zinc finger domain regarded hitherto as specific to eukaryotes. We demonstrated that AFV1p06 has ability to bind specifically to DNA sequences rich in GC. AFV1p06 is the first archaeal DNA binding protein with zinc finger domain characterized in vitro. The third transcriptional regulator, Sta1 is encoded by the genome of Sulfolobales. The protein RadA is able to activate the transcription of viral as well as chromosomal genes in response to DNA damage. To understand its role in the cell, we attempted, without success, to knockout the sta1 gene in S. islandicus RYE15A. This result indicates that the sta1 gene is probably essential. The strain S. islandicus LAL14 /1 is a model strain to study host-virus interaction in archaea. The sequencing of the genome of this strain opened the way to establish a genetic system for this model and allowed us to construct knockout mutants for several LAL14/1 genes (pyrEF-; ΔCRISPR1). Our unsuccessful attempts to inactivate topR2, another candidate gene encoding reverse gyrase indicate that topR2 function could be essential. The construction of the ΔCRISPR1 mutant opens the way to obtain a derivative of LAL14/1 entirely lacking the CRISPR system. Such a mutant will be very useful for the future studies of function and role of CRISPRs in archaea in general but also will allow to verify the hypothesis of involvement of CRISPRs in the phenotype of resistance of LA14/1 to SIRV1. All the results of this thesis contribute to an improved understanding of molecular mechanisms in archaeal cells and their viruses