Journal articles: 'Sulfolobales'

1

Berg, Ivan A., W. Hugo Ramos-Vera, Anna Petri, Harald Huber, and Georg Fuchs. "Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota." Microbiology 156, no. 1 (January 1, 2010): 256–69. http://dx.doi.org/10.1099/mic.0.034298-0.

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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.

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Romano, I., M. C. Manca, L. Lama, B. Nicolaus, and A. Gambacorta. "Method for antibiotic assay on Sulfolobales." Biotechnology Techniques 7, no. 7 (July 1993): 439–40. http://dx.doi.org/10.1007/bf00151880.

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Gomes, Cláudio M., Alice Faria, João C. Carita, Joaquim Mendes, Manuela Regalla, Paula Chicau, Harald Huber, Karl O. Stetter, and M. Teixeira. "Di-cluster, seven-iron ferredoxins from hyperthermophilic Sulfolobales." JBIC Journal of Biological Inorganic Chemistry 3, no. 5 (October 1998): 499–507. http://dx.doi.org/10.1007/s007750050260.

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Auernik, Kathryne S., and Robert M. Kelly. "Identification of Components of Electron Transport Chains in the Extremely Thermoacidophilic Crenarchaeon Metallosphaera sedula through Iron and Sulfur Compound Oxidation Transcriptomes." Applied and Environmental Microbiology 74, no. 24 (October 17, 2008): 7723–32. http://dx.doi.org/10.1128/aem.01545-08.

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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.

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Garrett, Roger A., Shiraz A. Shah, Gisle Vestergaard, Ling Deng, Soley Gudbergsdottir, Chandra S. Kenchappa, Susanne Erdmann, and Qunxin She. "CRISPR-based immune systems of the Sulfolobales: complexity and diversity." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 51–57. http://dx.doi.org/10.1042/bst0390051.

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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.

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Lemmens, Liesbeth, Kun Wang, Ebert Ruykens, Van Tinh Nguyen, Ann-Christin Lindås, Ronnie Willaert, Mohea Couturier, and Eveline Peeters. "DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius." Biomolecules 12, no. 4 (March 30, 2022): 524. http://dx.doi.org/10.3390/biom12040524.

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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.

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Satoh, Tomoko, Keiko Watanabe, Hideo Yamamoto, Shuichi Yamamoto, and Norio Kurosawa. "Archaeal Community Structures in the Solfataric Acidic Hot Springs with Different Temperatures and Elemental Compositions." Archaea 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/723871.

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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.

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Cannio, Raffaele, Gabriella Fiorentino, MosÃ¨ Rossi, and Simonetta Bartolucci. "The alcohol dehydrogenase gene: distribution among Sulfolobales and regulation inSulfolobus solfataricus." FEMS Microbiology Letters 170, no. 1 (January 1999): 31–39. http://dx.doi.org/10.1111/j.1574-6968.1999.tb13352.x.

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9

Zillig, Wolfram, Arnulf Kletzin, Christa Schleper, Ingelore Holz, Davorin Janekovic, Johannes Hain, Martin Lanzendörfer, and Jakob K. Kristjansson. "Screening for Sulfolobales, their Plasmids and their Viruses in Icelandic Solfataras." Systematic and Applied Microbiology 16, no. 4 (February 1993): 609–28. http://dx.doi.org/10.1016/s0723-2020(11)80333-4.

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10

Teufel, Robin, Johannes W. Kung, Daniel Kockelkorn, Birgit E. Alber, and Georg Fuchs. "3-Hydroxypropionyl-Coenzyme A Dehydratase and Acryloyl-Coenzyme A Reductase, Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in the Sulfolobales." Journal of Bacteriology 191, no. 14 (May 8, 2009): 4572–81. http://dx.doi.org/10.1128/jb.00068-09.

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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.

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Recalde, Alejandra, Marleen van Wolferen, Shamphavi Sivabalasarma, Sonja-Verena Albers, Claudio A. Navarro, and Carlos A. Jerez. "The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales." Microorganisms 9, no. 1 (January 18, 2021): 193. http://dx.doi.org/10.3390/microorganisms9010193.

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Polyphosphates (polyP) are polymers of orthophosphate residues linked by high-energy phosphoanhydride bonds that are important in all domains of life and function in many different processes, including biofilm development. To study the effect of polyP in archaeal biofilm formation, our previously described Sa. solfataricus polyP (−) strain and a new polyP (−) S. acidocaldarius strain generated in this report were used. These two strains lack the polymer due to the overexpression of their respective exopolyphosphatase gene (ppx). Both strains showed a reduction in biofilm formation, decreased motility on semi-solid plates and a diminished adherence to glass surfaces as seen by DAPI (4′,6-diamidino-2-phenylindole) staining using fluorescence microscopy. Even though arlB (encoding the archaellum subunit) was highly upregulated in S. acidocardarius polyP (−), no archaellated cells were observed. These results suggest that polyP might be involved in the regulation of the expression of archaellum components and their assembly, possibly by affecting energy availability, phosphorylation or other phenomena. This is the first evidence indicating polyP affects biofilm formation and other related processes in archaea.

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12

van Wolferen, Marleen, Xiaoqing Ma, and Sonja-Verena Albers. "DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales." Journal of Bacteriology 197, no. 18 (July 6, 2015): 2941–51. http://dx.doi.org/10.1128/jb.00344-15.

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ABSTRACTTheupsoperon ofSulfolobusspecies is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness ofSulfolobuscells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (saci_1497tosaci_1500) which encode proteins with putative DNA processing functions are present downstream of theupsoperon. In this study, we show that after UV treatment the cellular aggregation of strains withsaci_1497,saci_1498, andsaci_1500deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated thatsaci_1498, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded bysaci_1497nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, asaci_1500deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA ofSulfolobus acidocaldarius.IMPORTANCESulfolobalesspecies increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA betweenSulfolobuscells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism amongSulfolobalescells.

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Itoh, Takashi, Tatsuki Miura, Hiroyuki D. Sakai, Shingo Kato, Moriya Ohkuma, and Tomonori Takashina. "Sulfuracidifex tepidarius gen. nov., sp. nov. and transfer of Sulfolobus metallicus Huber and Stetter 1992 to the genus Sulfuracidifex as Sulfuracidifex metallicus comb. nov." International Journal of Systematic and Evolutionary Microbiology 70, no. 3 (March 1, 2020): 1837–42. http://dx.doi.org/10.1099/ijsem.0.003981.

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Two novel, strictly aerobic, sulfur-dependent, thermoacidophilic strains, IC-006T and IC-007, were isolated from a solfataric field at Hakone Ohwaku-dani, Kanagawa, Japan. Cells of the two strains were irregular cocci with a diameter of 1.0–1.8 µm. They were strict aerobes and grew in a temperature range between 45 and 69 °C (optimally at 65 °C) and a pH range between 0.4 and 5.5 (optimally at pH 3.5). They required sulfur or a reduced sulfur compound, and sulfur was oxidized to sulfate. They grew autotrophically or mixotrophically utilizing several sugars and complex organic substances as carbon sources. The DNA G+C content was 42.4 mol%. A comparison of the 16S rRNA gene sequences among members of the order Sulfolobales indicated that they were closely related to Sulfolobus metallicus , forming an independent lineage within this order. The two isolates and Sulfolobus metallicus were also diffentiated based on their phenotypic properties from the other members of the order Sulfolobales . Detailed comparisons of the phenotypic properties and DNA–DNA hybridization study illustrated that the two isolates belong to a species different from Sulfolobus metallicus . On the basis of the phylogenetic and phenotypic comparisons, we propose a new genus and species, Sulfuracidifex tepidarius gen. nov., sp. nov. to accommodate strains IC-006T and IC-007. The type strain of Sulfuracidifex tepidarius is IC-006T (=JCM 16833T=DSM 104736T). In addition, Sulfolobus metallicus should be transferred to the new genus as Sulfuracidifex metallicus comb. nov.: the type strain is Kra23T (=DSM 6482T=JCM 9184T=NBRC 15436T).

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Erdmann, Susanne, Shiraz A. Shah, and Roger A. Garrett. "SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2." Biochemical Society Transactions 41, no. 6 (November 20, 2013): 1449–58. http://dx.doi.org/10.1042/bst20130196.

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Organisms of the crenarchaeal order Sulfolobales carry complex CRISPR (clustered regularly interspaced short palindromic repeats) adaptive immune systems. These systems are modular and show extensive structural and functional diversity, especially in their interference complexes. The primary targets are an exceptional range of diverse viruses, many of which propagate stably within cells and follow lytic life cycles without producing cell lysis. These properties are consistent with the difficulty of activating CRISPR spacer uptake in the laboratory, but appear to conflict with the high complexity and diversity of the CRISPR immune systems that are found among the Sulfolobales. In the present article, we re-examine the first successful induction of archaeal spacer acquisition in our laboratory that occurred exclusively for the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2 that was co-infected with the virus SMV1 (Sulfolobus monocaudavirus 1). Although we reaffirm that protospacer selection is essentially a random process with respect to the pMGB1 genome, we identified single spacer sequences specific for each of CRISPR loci C, D and E that, exceptionally, occurred in many sequenced clones. Moreover, the same sequence was reproducibly acquired for a given locus in independent experiments, consistent with it being the first protospacer to be selected. There was also a small protospacer bias (1.6:1) to the antisense strand of protein genes. In addition, new experiments demonstrated that spacer acquisition in the previously inactive CRISPR locus A could be induced on freeze–thawing of the infected cells, suggesting that environmental stress can facilitate activation. Coincidentally with spacer acquisition, a mobile OrfB element was deleted from pMGB1, suggesting that interplay can occur between spacer acquisition and transposition.

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Auernik, Kathryne S., Yukari Maezato, Paul H. Blum, and Robert M. Kelly. "The Genome Sequence of the Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera sedula Provides Insights into Bioleaching-Associated Metabolism." Applied and Environmental Microbiology 74, no. 3 (December 14, 2007): 682–92. http://dx.doi.org/10.1128/aem.02019-07.

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ABSTRACT Despite their taxonomic description, not all members of the order Sulfolobales are capable of oxidizing reduced sulfur species, which, in addition to iron oxidation, is a desirable trait of biomining microorganisms. However, the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ∼2,300 open reading frames [ORFs]) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins involved (directly or indirectly) with bioleaching. As expected, the M. sedula genome contains genes related to autotrophic carbon fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence of hybrid quinol-cytochrome oxidase complexes. Comparisons with the mesophilic biomining bacterium Acidithiobacillus ferrooxidans ATCC 23270 indicate that the M. sedula genome encodes at least one putative rusticyanin, involved in iron oxidation, and a putative tetrathionate hydrolase, implicated in sulfur oxidation. The fox gene cluster, involved in iron oxidation in the thermoacidophilic archaeon Sulfolobus metallicus, was also identified. These iron- and sulfur-oxidizing components are missing from genomes of nonleaching members of the Sulfolobales, such as Sulfolobus solfataricus P2 and Sulfolobus acidocaldarius DSM 639. Whole-genome transcriptional response analysis showed that 88 ORFs were up-regulated twofold or more in M. sedula upon addition of ferrous sulfate to yeast extract-based medium; these included genes for components of terminal oxidase clusters predicted to be involved with iron oxidation, as well as genes predicted to be involved with sulfur metabolism. Many hypothetical proteins were also differentially transcribed, indicating that aspects of the iron and sulfur metabolism of M. sedula remain to be identified and characterized.

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Garrett, Roger, Shiraz Shah, Susanne Erdmann, Guannan Liu, Marzieh Mousaei, Carlos León-Sobrino, Wenfang Peng, et al. "CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity." Life 5, no. 1 (March 10, 2015): 783–817. http://dx.doi.org/10.3390/life5010783.

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Munson-McGee, Jacob H., Erin K. Field, Mary Bateson, Colleen Rooney, Ramunas Stepanauskas, and Mark J. Young. "Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs." Applied and Environmental Microbiology 81, no. 22 (September 4, 2015): 7860–68. http://dx.doi.org/10.1128/aem.01539-15.

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ABSTRACTNanoarchaeotaare obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence ofNanoarchaeotain high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposedNanobsidianus stetterifrom a more neutral YNP hot spring than to the marineNanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescencein situhybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNPNanoarchaeotaas aSulfolobalesspecies known to inhabit the hot springs. Furthermore, we demonstrate thatNanoarchaeotaare widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within oneNanoarchaeotasingle-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNPNanoarchaeota.

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Kurosawa, N., Y. H. Itoh, T. Iwai, A. Sugai, I. Uda, N. Kimura, T. Horiuchi, and T. Itoh. "Sulfurisphaera ohwakuensis gen. nov., sp. nov., a novel extremely thermophilic acidophile of the order Sulfolobales." International Journal of Systematic Bacteriology 48, no. 2 (April 1, 1998): 451–56. http://dx.doi.org/10.1099/00207713-48-2-451.

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Zink, Isabelle Anna, Erika Wimmer, and Christa Schleper. "Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales." Biomolecules 10, no. 11 (November 6, 2020): 1523. http://dx.doi.org/10.3390/biom10111523.

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Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.

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Bleriot, Yves, Edouard Untersteller, Benoit Fritz, and Pierre Sinay. "ChemInform Abstract: Total Synthesis of Calditol: Structural Clarification of This Typical Component of Archaea Order Sulfolobales." ChemInform 33, no. 21 (May 21, 2010): no. http://dx.doi.org/10.1002/chin.200221158.

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Hajj, Mirna, Petra Langendijk-Genevaux, Manon Batista, Yves Quentin, Sébastien Laurent, Régine Capeyrou, Ziad Abdel-Razzak, et al. "Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase." Biomolecules 11, no. 7 (June 26, 2021): 950. http://dx.doi.org/10.3390/biom11070950.

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Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.

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Serek-Heuberger, Justyna, Cédric F. V. Hobel, Stanislaw Dunin-Horkawicz, Beate Rockel, Jörg Martin, and Andrei N. Lupas. "Two unique membrane-bound AAA proteins from Sulfolobus solfataricus." Biochemical Society Transactions 37, no. 1 (January 20, 2009): 118–22. http://dx.doi.org/10.1042/bst0370118.

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Thermoacidophilic crenarchaea of the genus Sulfolobus contain six AAA (ATPase associated with various cellular activities) proteins, including a proteasome-associated ATPase, a Vps4 (vacuolar protein sorting 4) homologue, and two Cdc48 (cell-division cycle 48)-like proteins. The last two AAA proteins are deeply branching divergent members of this family without close relatives outside the Sulfolobales. Both proteins have two nucleotide-binding domains and, unlike other members of the family, they seem to lack folded N-terminal domains. Instead, they contain N-terminal extensions of approx. 50 residues, which are predicted to be unstructured, except for a single transmembrane helix. We have analysed the two proteins, MBA (membrane-bound AAA) 1 and MBA2, by computational and experimental means. They appear to be monophyletic and to share a common ancestor with the Cdc48 clade. Both are membrane-bound and active as nucleotidases upon heterologous expression in Escherichia coli. They form ring complexes, which are stable after solubilization in a mild detergent and whose formation is dependent on the presence of the N-terminal extensions.

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Prangishvili, D., and R. A. Garrett. "Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 204–8. http://dx.doi.org/10.1042/bst0320204.

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The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.

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Martusewitsch, Erika, Christoph W. Sensen, and Christa Schleper. "High Spontaneous Mutation Rate in the Hyperthermophilic Archaeon Sulfolobus solfataricus Is Mediated by Transposable Elements." Journal of Bacteriology 182, no. 9 (May 1, 2000): 2574–81. http://dx.doi.org/10.1128/jb.182.9.2574-2581.2000.

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ABSTRACT We have isolated uracil-auxotrophic mutants of the hyperthermophilic archaeon Sulfolobus solfataricus in order to explore the genomic stability and mutational frequencies of this organism and to identify complementable recipients for a selectable genetic transformation system. Positive selection of spontaneous mutants resistant to 5-fluoroorotate yielded uracil auxotrophs with frequencies of between 10−4 and 10−5 per sensitive, viable cell. Four different, nonhomologous insertion sequences (ISs) were identified at different positions within the chromosomal pyrEF locus of these mutants. They ranged in size from 1,058 to 1,439 bp and possessed properties typical of known transposable elements, i.e., terminal inverted repeats, flanking duplicated target sequences, and putative transposase genes encoding motifs that are indicative of the IS4-IS5 IS element families. Between 12 and 25 copies of each IS element were found in chromosomal DNAs by Southern analyses. While characteristic fingerprint patterns created by IS element-specific probes were observed with genomic DNA of different S. solfataricusstrains, no homologous sequences were identified in DNA of other well-characterized strains of the order Sulfolobales.

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Kockelkorn, Daniel, and Georg Fuchs. "Malonic Semialdehyde Reductase, Succinic Semialdehyde Reductase, and Succinyl-Coenzyme A Reductase from Metallosphaera sedula: Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Sulfolobales." Journal of Bacteriology 191, no. 20 (August 14, 2009): 6352–62. http://dx.doi.org/10.1128/jb.00794-09.

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ABSTRACT A 3-hydroxypropionate/4-hydroxybutyrate cycle operates during autotrophic CO2 fixation in various members of the Crenarchaea. In this cycle, as determined using Metallosphaera sedula, malonyl-coenzyme A (malonyl-CoA) and succinyl-CoA are reductively converted via their semialdehydes to the corresponding alcohols 3-hydroxypropionate and 4-hydroxybutyrate. Here three missing oxidoreductases of this cycle were purified from M. sedula and studied. Malonic semialdehyde reductase, a member of the 3-hydroxyacyl-CoA dehydrogenase family, reduces malonic semialdehyde with NADPH to 3-hydroxypropionate. The latter compound is converted via propionyl-CoA to succinyl-CoA. Succinyl-CoA reduction to succinic semialdehyde is catalyzed by malonyl-CoA/succinyl-CoA reductase, a promiscuous NADPH-dependent enzyme that is a paralogue of aspartate semialdehyde dehydrogenase. Succinic semialdehyde is then reduced with NADPH to 4-hydroxybutyrate by succinic semialdehyde reductase, an enzyme belonging to the Zn-dependent alcohol dehydrogenase family. Genes highly similar to the Metallosphaera genes were found in other members of the Sulfolobales. Only distantly related genes were found in the genomes of autotrophic marine Crenarchaeota that may use a similar cycle in autotrophic carbon fixation.

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Fuchs, Tanja, Harald Huber, Siegfried Burggraf, and Karl O. Stetter. "16S rDNA-based Phylogeny of the Archaeal Order Sulfolobales and Reclassification of Desulfurolobus ambivalens as Acidianus ambivalens comb. nov." Systematic and Applied Microbiology 19, no. 1 (March 1996): 56–60. http://dx.doi.org/10.1016/s0723-2020(96)80009-9.

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Segerer, A. H., A. Trincone, M. Gahrtz, and K. O. Stetter. "Stygiolobus azoricus gen. nov., sp. nov. Represents a Novel Genus of Anaerobic, Extremely Thermoacidophilic Archaebacteria of the Order Sulfolobales." International Journal of Systematic Bacteriology 41, no. 4 (October 1, 1991): 495–501. http://dx.doi.org/10.1099/00207713-41-4-495.

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Trevisanato, Siro I., Niels Larsen, Andreas H. Segerer, Karl O. Stetter, and Roger A. Garrett. "Phylogenetic Analysis of the Archaeal Order of Sulfolobales Based on Sequences of 23S rRNA Genes and 16S/23S rDNA Spacers." Systematic and Applied Microbiology 19, no. 1 (March 1996): 61–65. http://dx.doi.org/10.1016/s0723-2020(96)80010-5.

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Guo, Xin, and Li Huang. "A Superfamily 3 DNA Helicase Encoded by Plasmid pSSVi from the Hyperthermophilic Archaeon Sulfolobus solfataricus Unwinds DNA as a Higher-Order Oligomer and Interacts with Host Primase." Journal of Bacteriology 192, no. 7 (January 29, 2010): 1853–64. http://dx.doi.org/10.1128/jb.01300-09.

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ABSTRACT Replication proteins encoded by nonconjugative plasmids from the hyperthermophilic archaea of the order Sulfolobales show great diversity in amino acid sequence. We have biochemically characterized ORF735, a replication protein from pSSVi, an integrative nonconjugative plasmid from Sulfolobus solfataricus P2. We show that ORF735 is a DNA helicase of superfamily 3. It unwound double-stranded DNA (dsDNA) in a 3′-to-5′ direction in the presence of ATP over a wide range of temperatures, from 37°C to 75°C, and possessed DNA-stimulated ATPase activity. ORF735 existed in solution as a salt-stable dimer and was capable of assembling into a salt-sensitive oligomer that was significantly larger than a hexamer in the presence of a divalent cation (Mg2+) and an adenine nucleotide (ATP, dATP, or ADP) or its analog (ATPγS or AMPPNP). Both N-terminal and C-terminal portions of ORF735 (87 and 160 amino acid residues, respectively, in size) were required for protein dimerization but dispensable for the formation of the higher-order oligomer. The protein unwound DNA only as a large oligomer. Yeast two-hybrid and coimmunoprecipitation assays revealed that ORF735 interacted with the noncatalytic subunit of host primase. These findings provide clues to the functional role of ORF735 in pSSVi DNA replication.

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Miyabayashi, Hiroka, Hiroyuki D. Sakai, and Norio Kurosawa. "DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme PolB1 in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius." Microorganisms 9, no. 2 (February 20, 2021): 439. http://dx.doi.org/10.3390/microorganisms9020439.

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DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, two subunits, PolB1-binding protein (PBP)1 and PBP2, were identified in Saccharolobus solfataricus. Previous in vitro studies suggested that PBP1 and PBP2 influence the core activity of apoenzyme PolB1 (apo-PolB1). PBP1 contains a C-terminal acidic tail and modulates the strand-displacement synthesis activity of PolB1 during the synthesis of Okazaki fragments. PBP2 modestly enhances the DNA polymerase activity of apo-PolB1. These subunits are present in Sulfolobales, Acidilobales, and Desulfurococcales, which belong to Crenarchaea. However, it has not been determined whether these subunits are essential for the activity of apo-PolB1. In this study, we constructed a pbp1 deletion strain in S. acidocaldarius and characterized its phenotypes. However, a pbp2 deletion strain was not obtained, indicating that PBP2 is essential for replication by holoenzyme PolB1. A pbp1 deletion strain was sensitive to various types of DNA damage and exhibited an increased mutation rate, suggesting that PBP1 contribute to the repair or tolerance of DNA damage by holoenzyme PolB1. The results of our study suggest that PBP1 is important for DNA repair by holoenzyme PolB1 in S. acidocaldarius.

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Wolters, Jörn, and Volker A. Erdmann. "The structure and evolution of archaebacterial ribosomal RNAs." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 43–51. http://dx.doi.org/10.1139/m89-007.

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A cladistic analysis of 553 5S rRNA sequences has revealed a Ur-5S rRNA, the ancestor of all present-day 5S rRNA molecules. Previously stated characteristic differences between the eubacterial and eukaryotic molecules, namely, the length base-pairing schemes of helices D, can be used as a marker for the various archaebacterial branches. One model comprises Thermococcus, Thermoplasma, methanobacteria, and halobacteria; a second comprises the Sulfolobales; and a third is represented only by the single organism Octopus Spring species 1. A relaxed selection pressure on helix E with subsequent deletions is observed in Methanobacteriales, Methanococcales, and eubacteria. The secondary structures are supported by enzymatic digestion and chemical modification studies of the 5S rRNAs. Reconstitution of eubacterial 50S ribosomal subunits with 5S rRNA from Halobacterium and Thermoplasma has revealed 100% incorporation, while eukaryotic 5S rRNAs yielded a 50% incorporation. Relevant positions of the small-subunit rRNA are selected to answer the question of the monophyly of archaebacteria. Eight positions account for monophyly, eight for an ancestry of eubacteria with halophile methanogens and eukaryotes with eocytes (paraphyly of archaebacteria), and two for an ancestry of eubacteria with eocytes. A refinement of the neighborliness method of S. Sattath and A. Tversky resulted in a monophyly of archaebacteria when all positions are treated equally and in a paraphyly when tranversions are weighted twice over transitions.Key words: archaebacteria, ribosomal RNA, evolution, cladistic analysis.

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Sakai, Hiroyuki D., and Norio Kurosawa. "Sulfodiicoccus acidiphilus gen. nov., sp. nov., a sulfur-inhibited thermoacidophilic archaeon belonging to the order Sulfolobales isolated from a terrestrial acidic hot spring." International Journal of Systematic and Evolutionary Microbiology 67, no. 6 (June 1, 2017): 1880–86. http://dx.doi.org/10.1099/ijsem.0.001881.

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Zeng, Zhirui, Xiao-Lei Liu, Jeremy H. Wei, Roger E. Summons, and Paula V. Welander. "Calditol-linked membrane lipids are required for acid tolerance inSulfolobus acidocaldarius." Proceedings of the National Academy of Sciences 115, no. 51 (December 5, 2018): 12932–37. http://dx.doi.org/10.1073/pnas.1814048115.

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Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radicalS-adenosylmethionine (SAM) protein inSulfolobus acidocaldariusrequired for the synthesis of a unique cyclopentyl head group, known as calditol. Calditol-linked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol–GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis rendersS. acidocaldariussensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress.

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Ramos-Vera, W. Hugo, Ivan A. Berg, and Georg Fuchs. "Autotrophic Carbon Dioxide Assimilation in Thermoproteales Revisited." Journal of Bacteriology 191, no. 13 (May 1, 2009): 4286–97. http://dx.doi.org/10.1128/jb.00145-09.

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ABSTRACT For Crenarchaea, two new autotrophic carbon fixation cycles were recently described. Sulfolobales use the 3-hydroxypropionate/4-hydroxybutyrate cycle, with acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme. Ignicoccus hospitalis (Desulfurococcales) uses the dicarboxylate/4-hydroxybutyrate cycle, with pyruvate synthase and phosphoenolpyruvate carboxylase being responsible for CO2 fixation. In the two cycles, acetyl-CoA and two inorganic carbons are transformed to succinyl-CoA by different routes, whereas the regeneration of acetyl-CoA from succinyl-CoA proceeds via the same route. Thermoproteales would be an exception to this unifying concept, since for Thermoproteus neutrophilus, the reductive citric acid cycle was proposed as a carbon fixation mechanism. Here, evidence is presented for the operation of the dicarboxylate/4-hydroxybutyrate cycle in this archaeon. All required enzyme activities were detected in large amounts. The key enzymes of the cycle were strongly upregulated under autotrophic growth conditions, indicating their involvement in autotrophic CO2 fixation. The corresponding genes were identified in the genome. 14C-labeled 4-hydroxybutyrate was incorporated into the central building blocks in accordance with the key position of this compound in the cycle. Moreover, the results of previous 13C-labeling studies, which could be reconciled with a reductive citric acid cycle only when some assumptions were made, were perfectly in line with the new proposal. We conclude that the dicarboxylate/4-hydroxybutyrate cycle is operating in CO2 fixation in the strict anaerobic Thermoproteales as well as in Desulfurococcales.

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Muller, Sébastien, Alan Urban, Arnaud Hecker, Fabrice Leclerc, Christiane Branlant, and Yuri Motorin. "Deficiency of the tRNA Tyr :Ψ35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery." Nucleic Acids Research 37, no. 4 (January 12, 2009): 1308–22. http://dx.doi.org/10.1093/nar/gkn1037.

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Stieglmeier, Michaela, Andreas Klingl, Ricardo J. E. Alves, Simon K. M. R. Rittmann, Michael Melcher, Nikolaus Leisch, and Christa Schleper. "Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota." International Journal of Systematic and Evolutionary Microbiology 64, Pt_8 (August 1, 2014): 2738–52. http://dx.doi.org/10.1099/ijs.0.063172-0.

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A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76T, was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6–0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76T had an S-layer with p3 symmetry, so far only reported for members of the Sulfolobales . Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids. The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively. The genome of strain EN76T had a DNA G+C content of 52.7 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain EN76T is affiliated with the recently proposed phylum Thaumarchaeota , sharing 85 % 16S rRNA gene sequence identity with the closest cultivated relative ‘Candidatus Nitrosopumilus maritimus’ SCM1, a marine ammonia-oxidizing archaeon, and a maximum of 81 % 16S rRNA gene sequence identity with members of the phyla Crenarchaeota and Euryarchaeota and any of the other recently proposed phyla (e.g. ‘Korarchaeota’ and ‘Aigarchaeota’). We propose the name Nitrososphaera viennensis gen. nov., sp. nov. to accommodate strain EN76T. The type strain of Nitrososphaera viennensis is strain EN76T ( = DSM 26422T = JMC 19564T). Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.

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Alber, Birgit, Marc Olinger, Annika Rieder, Daniel Kockelkorn, Björn Jobst, Michael Hügler, and Georg Fuchs. "Malonyl-Coenzyme A Reductase in the Modified 3-Hydroxypropionate Cycle for Autotrophic Carbon Fixation in Archaeal Metallosphaera and Sulfolobus spp." Journal of Bacteriology 188, no. 24 (October 13, 2006): 8551–59. http://dx.doi.org/10.1128/jb.00987-06.

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ABSTRACT Autotrophic members of the Sulfolobales (Crenarchaeota) contain acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the CO2 fixation enzyme and use a modified 3-hydroxypropionate cycle to assimilate CO2 into cell material. In this central metabolic pathway malonyl-CoA, the product of acetyl-CoA carboxylation, is further reduced to 3-hydroxypropionate. Extracts of Metallosphaera sedula contained NADPH-specific malonyl-CoA reductase activity that was 10-fold up-regulated under autotrophic growth conditions. Malonyl-CoA reductase was partially purified and studied. Based on N-terminal amino acid sequencing the corresponding gene was identified in the genome of the closely related crenarchaeum Sulfolobus tokodaii. The Sulfolobus gene was cloned and heterologously expressed in Escherichia coli, and the recombinant protein was purified and studied. The enzyme catalyzes the following reaction: malonyl-CoA + NADPH + H+ → malonate-semialdehyde + CoA + NADP+. In its native state it is associated with small RNA. Its activity was stimulated by Mg2+ and thiols and inactivated by thiol-blocking agents, suggesting the existence of a cysteine adduct in the course of the catalytic cycle. The enzyme was specific for NADPH (Km = 25 μM) and malonyl-CoA (Km = 40 μM). Malonyl-CoA reductase has 38% amino acid sequence identity to aspartate-semialdehyde dehydrogenase, suggesting a common ancestor for both proteins. It does not exhibit any significant similarity with malonyl-CoA reductase from Chloroflexus aurantiacus. This shows that the autotrophic pathway in Chloroflexus and Sulfolobaceae has evolved convergently and that these taxonomic groups have recruited different genes to bring about similar metabolic processes.

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Kozubal, M., R. E. Macur, S. Korf, W. P. Taylor, G. G. Ackerman, A. Nagy, and W. P. Inskeep. "Isolation and Distribution of a Novel Iron-Oxidizing Crenarchaeon from Acidic Geothermal Springs in Yellowstone National Park." Applied and Environmental Microbiology 74, no. 4 (December 14, 2007): 942–49. http://dx.doi.org/10.1128/aem.01200-07.

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ABSTRACT Novel thermophilic crenarchaea have been observed in Fe(III) oxide microbial mats of Yellowstone National Park (YNP); however, no definitive work has identified specific microorganisms responsible for the oxidation of Fe(II). The objectives of the current study were to isolate and characterize an Fe(II)-oxidizing member of the Sulfolobales observed in previous 16S rRNA gene surveys and to determine the abundance and distribution of close relatives of this organism in acidic geothermal springs containing high concentrations of dissolved Fe(II). Here we report the isolation and characterization of the novel, Fe(II)-oxidizing, thermophilic, acidophilic organism Metallosphaera sp. strain MK1 obtained from a well-characterized acid-sulfate-chloride geothermal spring in Norris Geyser Basin, YNP. Full-length 16S rRNA gene sequence analysis revealed that strain MK1 exhibits only 94.9 to 96.1% sequence similarity to other known Metallosphaera spp. and less than 89.1% similarity to known Sulfolobus spp. Strain MK1 is a facultative chemolithoautotroph with an optimum pH range of 2.0 to 3.0 and an optimum temperature range of 65 to 75°C. Strain MK1 grows optimally on pyrite or Fe(II) sorbed onto ferrihydrite, exhibiting doubling times between 10 and 11 h under aerobic conditions (65°C). The distribution and relative abundance of MK1-like 16S rRNA gene sequences in 14 acidic geothermal springs containing Fe(III) oxide microbial mats were evaluated. Highly related MK1-like 16S rRNA gene sequences (>99% sequence similarity) were consistently observed in Fe(III) oxide mats at temperatures ranging from 55 to 80°C. Quantitative PCR using Metallosphaera-specific primers confirmed that organisms highly similar to strain MK1 comprised up to 40% of the total archaeal community at selected sites. The broad distribution of highly related MK1-like 16S rRNA gene sequences in acidic Fe(III) oxide microbial mats is consistent with the observed characteristics and growth optima of Metallosphaera-like strain MK1 and emphasizes the importance of this newly described taxon in Fe(II) chemolithotrophy in acidic high-temperature environments of YNP.

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De Maio, Anna, Elena Porzio, Sergio Rotondo, Anna Rita Bianchi, and Maria Rosaria Faraone-Mennella. "In Sulfolobus solfataricus, the Poly(ADP-Ribose) Polymerase-Like Thermoprotein Is a Multifunctional Enzyme." Microorganisms 8, no. 10 (October 3, 2020): 1523. http://dx.doi.org/10.3390/microorganisms8101523.

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In Sulfolobus solfataricus, Sso, the ADP-ribosylating thermozyme is known to carry both auto- and heteromodification of target proteins via short chains of ADP-ribose. Here, we provide evidence that this thermoprotein is a multifunctional enzyme, also showing ATPase activity. Electrophoretic and kinetic analyses were performed using NAD+ and ATP as substrates. The results showed that ATP is acting as a negative effector on the NAD+-dependent reaction, and is also responsible for inducing the dimerization of the thermozyme. These findings enabled us to further investigate the kinetic of ADP-ribosylation activity in the presence of ATP, and to also assay its ability to work as a substrate. Moreover, since the heteroacceptor of ADP-ribose is the sulfolobal Sso7 protein, known as an ATPase, some reconstitution experiments were set up to study the reciprocal influence of the ADP-ribosylating thermozyme and the Sso7 protein on their activities, considering also the possibility of direct enzyme/Sso7 protein interactions. This study provides new insights into the ATP-ase activity of the ADP-ribosylating thermozyme, which is able to establish stable complexes with Sso7 protein.

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Liu, Li-Jun, Zhen Jiang, Pei Wang, Ya-Ling Qin, Wen Xu, Yang Wang, Shuang-Jiang Liu, and Cheng-Ying Jiang. "Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea." Frontiers in Microbiology 12 (October 14, 2021). http://dx.doi.org/10.3389/fmicb.2021.768283.

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The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.

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Fernandes-Martins, Maria C., Daniel R. Colman, and Eric S. Boyd. "Sulfide oxidation by members of the Sulfolobales." PNAS Nexus, May 23, 2024. http://dx.doi.org/10.1093/pnasnexus/pgae201.

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Abstract The oxidation of sulfur compounds drives the acidification of geothermal waters. At high temperatures (>80°C) and in acidic conditions (pH <6.0), oxidation of sulfide has historically been considered an abiotic process that generates elemental sulfur (S0) that, in turn, is oxidized by thermoacidophiles of the model archaeal order Sulfolobales to generate sulfuric acid (i.e., sulfate and protons). Here, we describe five new aerobic and autotrophic strains of Sulfolobales comprising two species that were isolated from acidic hot springs in Yellowstone National Park (YNP) and that can use sulfide as an electron donor. These strains significantly accelerated the rate and extent of sulfide oxidation to sulfate relative to abiotic controls, concomitant with production of cells. Yields of sulfide-grown cultures were ∼2-fold greater than those of S0-grown cultures, consistent with thermodynamic calculations indicating more available energy in the former condition than the latter. Homologs of sulfide:quinone oxidoreductase (Sqr) were identified in nearly all Sulfolobales genomes from YNP metagenomes as well as those from other reference Sulfolobales, suggesting a widespread ability to accelerate sulfide oxidation. These observations expand the role of Sulfolobales in the oxidative sulfur cycle, the geobiological feedbacks that drive the formation of acidic hot springs, and landscape evolution.

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Omokawa, Hiromi, Norio Kurosawa, Shingo Kato, Takashi Itoh, Moriya Ohkuma, and Hiroyuki D. Sakai. "Complete Genome Sequence of a Novel Sulfolobales Archaeon Strain, HS-7, Isolated from the Unzen Hot Spring in Japan." Microbiology Resource Announcements 10, no. 38 (September 23, 2021). http://dx.doi.org/10.1128/mra.00582-21.

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The order Sulfolobales includes thermoacidophilic archaea that thrive in acidic geothermal environments. A novel Sulfolobales archaeon strain, HS-7, which may represent a novel genus, was isolated from an acidic hot spring in Japan. We report the 2.15-Mb complete genome sequence of strain HS-7.

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De Kock, Veerke, Eveline Peeters, and Rani Baes. "The Lrs14 family of DNA‐binding proteins as nucleoid‐associated proteins in the Crenarchaeal order Sulfolobales." Molecular Microbiology, April 3, 2024. http://dx.doi.org/10.1111/mmi.15260.

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AbstractOrganization of archaeal chromatin combines bacterial, eukaryotic, and unique characteristics. Many archaeal lineages harbor a wide diversity of small and highly expressed nucleoid‐associated proteins, which are involved in DNA structuring. In Sulfolobales, representing model organisms within the Crenarchaeota, Sul7d, Cren7, Sul10a, and Sul12a are well‐characterized nucleoid‐associated proteins. Here, we combine evidence that the Lrs14 family of DNA binders is part of the repertoire of nucleoid‐associated proteins in Sulfolobales. Lrs14‐encoding genes are widespread within genomes of different members of the Sulfolobales, typically encoded as four to nine homologs per genome. The Lrs14 proteins harbor a winged helix‐turn‐helix DNA‐binding domain and are typified by a coiled–coil dimerization. They are characterized by distinct sequence‐ and structure‐based features, including redox‐sensitive motifs and residues targeted for posttranslational modification, allowing a further classification of the family into five conserved clusters. Lrs14‐like proteins have unique DNA‐organizing properties. By binding to the DNA nonsequence specifically and in a highly cooperative manner, with a slight preference for AT‐rich promoter regions, they introduce DNA kinks and are able to affect transcription of adjacent transcription units either positively or negatively. Genes encoding Lrs14‐type proteins display considerable differential expression themselves in response to various stress conditions, with certain homologs being specific to a particular stressor. Taken together, we postulate that members of the Lrs14 family can be considered nucleoid‐associated proteins in Sulfolobales, combining a DNA‐structuring role with a global gene expression role in response to stress conditions.

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"The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79." International Journal of Systematic and Evolutionary Microbiology 55, no. 1 (January 1, 2005): 517–18. http://dx.doi.org/10.1099/ijs.0.63548-0.

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The Judicial Commission of the International Committee on Systematics of Prokaryotes has corrected the nomenclatural types of 12 orders: Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales.

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Medvedeva, Sofia, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili, and Mart Krupovic. "Virus-borne mini-CRISPR arrays are involved in interviral conflicts." Nature Communications 10, no. 1 (November 15, 2019). http://dx.doi.org/10.1038/s41467-019-13205-2.

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AbstractCRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.

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Xuyang, Li, Lozano-Madueño Cristina, Martínez-Alvarez Laura, and Peng Xu. "A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression." Nucleic Acids Research, February 2, 2023. http://dx.doi.org/10.1093/nar/gkad011.

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Abstract Cell cycle regulation is crucial for all living organisms and is often targeted by viruses to facilitate their own propagation, yet cell cycle progression control is largely underexplored in archaea. In this work, we reveal a cell cycle regulator (aCcr1) carrying a ribbon-helix-helix (RHH) domain and ubiquitous in the Thermoproteota of the order Sulfolobales and their viruses. Overexpression of several aCcr1 members including gp21 of rudivirus SIRV2 and its host homolog SiL_0190 of Saccharolobus islandicus LAL14/1 results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in cellular DNA content. Additionally, both gp21 and SiL_0190 can bind to the motif AGTATTA conserved in the promoter of several genes involved in cell division, DNA replication and cellular metabolism thereby repressing or inducing their transcription. Our results suggest that aCcr1 silences cell division and drives progression to the S-phase in Sulfolobales, a function exploited by viruses to facilitate viral propagation.

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van Wolferen, Marleen, Asif Shajahan, Kristina Heinrich, Susanne Brenzinger, Ian M. Black, Alexander Wagner, Ariane Briegel, Parastoo Azadi, and Sonja-Verena Albers. "Species-Specific Recognition of Sulfolobales Mediated by UV-Inducible Pili and S-Layer Glycosylation Patterns." mBio 11, no. 2 (March 10, 2020). http://dx.doi.org/10.1128/mbio.03014-19.

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ABSTRACT The UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA to repair DNA double-strand breaks via homologous recombination. Substitution of the Sulfolobus acidocaldarius pilin subunits UpsA and UpsB with their homologs from Sulfolobus tokodaii showed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance of N-glycosylation in the recognition process. In addition, the N-glycan decorating the S-layer of S. tokodaii is different from the one of S. acidocaldarius. Therefore, each Sulfolobus species seems to have developed a unique UpsA binding pocket and unique N-glycan composition to ensure aggregation and, consequently, also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination. IMPORTANCE Type IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The UV-inducible pili system of Sulfolobales (Ups) pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, thereby assisting in genome stability. With this work, we show that different Sulfolobus species have specific regions in their Ups pili subunits, which allow them to interact only with cells from the same species. Additionally, different Sulfolobus species have unique surface-layer N-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.

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Liu, Li, Philip C. Brown, Martin Könneke, Harald Huber, Simone König, and Ivan A. Berg. "Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota." mSphere 6, no. 1 (February 24, 2021). http://dx.doi.org/10.1128/msphere.01079-20.

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Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaea of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments.

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Marín-Paredes, Roberto, Yunuen Tapia-Torres, Esperanza Martínez-Romero, Mauricio Quesada, and Luis E. Servín-Garcidueñas. "Metagenome Assembly and Metagenome-Assembled Genome of “ Candidatus Aramenus sulfurataquae” from Thermal Sediments from the Los Azufres Volcanic Complex." Microbiology Resource Announcements 10, no. 39 (September 30, 2021). http://dx.doi.org/10.1128/mra.00379-21.

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A plethora of hot springs are found at the Los Azufres volcanic complex in Mexico, and studies are needed to determine their microbial genomic diversity. Here, we report a metagenome of hot spring sediments and a metagenome-assembled genome of “ Candidatus Aramenus sulfurataquae.” This study reveals novel genomic sequences of Sulfolobales archaea.

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Bertran, Emma, Lewis M. Ward, and David T. Johnston. "Draft Genome Sequence of Acidianus ambivalens DSM 3772, an Aerobic Thermoacidophilic Sulfur Disproportionator." Microbiology Resource Announcements 9, no. 3 (January 16, 2020). http://dx.doi.org/10.1128/mra.01415-19.

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Here, we describe the genome sequence of Acidianus ambivalens DSM 3772, an archaeon belonging to the Sulfolobales order that was first isolated from continental solfataric fields. This thermoacidophile was sequenced because it utilizes a unique sulfur disproportionation pathway that enables this metabolism under aerobic conditions, in contrast to obligately anaerobic bacterial sulfur disproportionators.

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Journal articles on the topic 'Sulfolobales'

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