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1.
World J Microbiol Biotechnol ; 36(3): 51, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-32157408

RESUMO

Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.


Assuntos
Celulase/genética , Celulase/metabolismo , Celulose/metabolismo , DNA , Genômica , Água/metabolismo , Sequência de Aminoácidos , Archaea/enzimologia , Archaea/genética , Bactérias/enzimologia , Bactérias/genética , Sequência de Bases , Clonagem Molecular , Estabilidade Enzimática , Escherichia coli/genética , Concentração de Íons de Hidrogênio , Peso Molecular , Filipinas , Proteínas Recombinantes , Alinhamento de Sequência , Sulfolobales/enzimologia , Sulfolobales/genética , Temperatura , Microbiologia da Água
2.
Appl Environ Microbiol ; 81(22): 7860-8, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26341207

RESUMO

Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in 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 proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.


Assuntos
Fontes Termais/microbiologia , Nanoarchaeota/fisiologia , Nanoarchaeota/virologia , Sulfolobales/fisiologia , Fontes Termais/virologia , Metagenômica , Nanoarchaeota/classificação , Nanoarchaeota/genética , Parques Recreativos , RNA Ribossômico 16S/genética , Análise de Célula Única , Sulfolobales/genética , Wyoming
3.
J Bacteriol ; 197(18): 2941-51, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26148716

RESUMO

UNLABELLED: The ups operon of Sulfolobus species 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 of Sulfolobus cells 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_1497 to saci_1500) which encode proteins with putative DNA processing functions are present downstream of the ups operon. In this study, we show that after UV treatment the cellular aggregation of strains with saci_1497, saci_1498, and saci_1500 deletions 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 that saci_1498, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by saci_1497 nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a saci_1500 deletion 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 of Sulfolobus acidocaldarius. IMPORTANCE: Sulfolobales species 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 between Sulfolobus cells 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 among Sulfolobales cells.


Assuntos
Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica/efeitos da radiação , Estresse Fisiológico/efeitos da radiação , Sulfolobales/metabolismo , Sulfolobales/efeitos da radiação , Raios Ultravioleta , Proteínas de Bactérias/genética , DNA Bacteriano , Sulfolobales/genética
4.
Environ Microbiol ; 17(5): 1600-14, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25142282

RESUMO

Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.


Assuntos
Archaea/metabolismo , Sedimentos Geológicos/microbiologia , Éteres de Glicerila/metabolismo , Fontes Termais/microbiologia , Lipídeos de Membrana/metabolismo , Archaea/genética , Desulfurococcales/genética , Desulfurococcales/isolamento & purificação , Meio Ambiente , Éteres de Glicerila/análise , Concentração de Íons de Hidrogênio , Lipídeos de Membrana/análise , Oxigênio/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Estações do Ano , Microbiologia do Solo , Sulfolobales/genética , Sulfolobales/isolamento & purificação , Temperatura , Thermoplasmales/genética , Thermoplasmales/isolamento & purificação , Tibet
5.
Archaea ; 2013: 723871, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23710131

RESUMO

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.


Assuntos
Archaea/classificação , Archaea/genética , Fontes Termais/microbiologia , Consórcios Microbianos , Sequência de Bases , Biodiversidade , DNA Arqueal/genética , Genes Arqueais , Japão , Consórcios Microbianos/genética , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfolobales/classificação , Sulfolobales/genética , Temperatura
6.
Biol Direct ; 8: 9, 2013 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-23607440

RESUMO

BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.


Assuntos
Proteínas Arqueais/genética , Genoma Arqueal , Nanoarchaeota/fisiologia , Sulfolobales/fisiologia , Simbiose , Proteínas Arqueais/metabolismo , Evolução Biológica , Evolução Molecular , Dados de Sequência Molecular , Nanoarchaeota/genética , Filogenia , Reação em Cadeia da Polimerase , Homologia de Sequência , Sulfolobales/genética , Wyoming
7.
FEMS Microbiol Ecol ; 85(3): 452-64, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23607726

RESUMO

The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.


Assuntos
Archaea/classificação , Bactérias/classificação , Fontes Termais/microbiologia , Archaea/genética , Archaea/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodiversidade , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Fontes Termais/química , Temperatura Alta , Filipinas , Filogenia , RNA Ribossômico 16S/genética , Sulfolobales/genética , Sulfolobales/isolamento & purificação , Sulfolobales/metabolismo , Enxofre/metabolismo
8.
RNA Biol ; 10(5): 891-9, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23403393

RESUMO

Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2-5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers and their insertion into CRISPR loci. Subsequently, evidence accumulated from different virus- and plasmid-targeting assays, suggesting that these motifs were also recognized during DNA interference, at least for the recently classified type I and type II CRISPR-based systems. The two processes, spacer acquisition and protospacer interference, employ different molecular mechanisms, and there is increasing evidence to suggest that the sequence motifs that are recognized, while overlapping, are unlikely to be identical. In this article, we consider the properties of PAM sequences and summarize the evidence for their dual functional roles. It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites.


Assuntos
Archaea/genética , Bactérias/genética , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Motivos de Nucleotídeos , Archaea/metabolismo , Bactérias/metabolismo , Sequência de Bases , DNA Intergênico , DNA Viral/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Dados de Sequência Molecular , Plasmídeos , Sulfolobales/genética , Sulfolobales/metabolismo
9.
Environ Microbiol ; 15(4): 1160-75, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23126508

RESUMO

Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.


Assuntos
Archaea/classificação , Bactérias/classificação , Variação Genética/genética , Fontes Termais/microbiologia , Desequilíbrio Ácido-Base , Archaea/genética , Bactérias/genética , China , Crenarchaeota/genética , Genes de RNAr , Fontes Termais/química , Filogenia , Proteobactérias/genética , RNA Ribossômico 16S/genética , Especificidade da Espécie , Sulfolobales/genética , Temperatura , Tibet
10.
Biochem Soc Trans ; 39(1): 51-7, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21265746

RESUMO

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.


Assuntos
Imunidade/genética , Sequências Repetidas Invertidas , Sulfolobales/genética , Sulfolobales/imunologia , Proteínas Arqueais/classificação , Proteínas Arqueais/genética , Proteínas Arqueais/imunologia , Sequência de Bases , DNA Bacteriano/genética , DNA Bacteriano/imunologia , DNA Intergênico , DNA Viral/genética , DNA Viral/imunologia , Dados de Sequência Molecular
11.
Mol Microbiol ; 73(1): 58-72, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19522740

RESUMO

The cell walls of Sulfolobales species consist of proteinaceous S-layers assembled from two polypeptides, SlaA and SlaB. We isolated the large S-layer protein of Acidianus ambivalens and both S-layer subunits of Sulfolobus solfataricus and Metallosphaera sedula, respectively. The slaAB genes, lying adjacently in the chromosomes, are constitutively transcribed as bicistronic operons in A. ambivalens and S. solfataricus. A smaller slaA transcript appeared in Northern hybridizations of A. ambivalens RNA. PCRs experiments showed that 80-85% of the transcripts stop at an oligo-T terminator downstream of slaA while 15-20% are read through to a second terminator downstream of slaB. The bicistronic operons including promoter and terminator regions are conserved in the Sulfolobales. While no SlaA homologue is found outside the Sulfolobales, SlaB is distantly similar to S-layer proteins of other Crenarchaeota, e.g. the Staphylothermus marinus tetrabrachion. Molecular modelling suggests SlaBs to be composed of 2-3 consecutive beta sandwich domains, a coiled-coil domain of 15-17 nm in length and a C-terminal transmembrane helix. Electron microscopy shows crystalline protein arrays with triangular and hexagonal pores. We propose that the mushroom-shaped 'unit cells' of the Sulfolobales' S-layers consist of three SlaBs anchoring the complex in the membrane and six SlaAs forming the detergent-resistant outer sacculus.


Assuntos
Proteínas Arqueais/metabolismo , Glicoproteínas de Membrana/metabolismo , Sulfolobales/genética , Sequência de Aminoácidos , Proteínas Arqueais/genética , Sequência de Bases , Regulação da Expressão Gênica em Archaea , Glicoproteínas de Membrana/genética , Modelos Moleculares , Dados de Sequência Molecular , Óperon , Regiões Promotoras Genéticas , Estrutura Terciária de Proteína , RNA Arqueal/genética , Alinhamento de Sequência , Sulfolobales/metabolismo , Regiões Terminadoras Genéticas
12.
J Bacteriol ; 191(14): 4572-81, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19429610

RESUMO

A 3-hydroxypropionate/4-hydroxybutyrate cycle operates in autotrophic CO(2) 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.


Assuntos
Acil Coenzima A/metabolismo , Proteínas Arqueais/metabolismo , Enoil-CoA Hidratase/metabolismo , Hidroxibutiratos/metabolismo , Oxirredutases/metabolismo , Propionatos/metabolismo , Sulfolobales/enzimologia , Proteínas Arqueais/isolamento & purificação , Enoil-CoA Hidratase/genética , Enoil-CoA Hidratase/isolamento & purificação , Genes Arqueais , Redes e Vias Metabólicas , Modelos Biológicos , NADP/metabolismo , Oxirredutases/genética , Oxirredutases/isolamento & purificação , Homologia de Sequência de Aminoácidos , Sulfolobales/genética
13.
Nucleic Acids Res ; 37(4): 1308-22, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-19139072

RESUMO

Up to now, Psi formation in tRNAs was found to be catalysed by stand-alone enzymes. By computational analysis of archaeal genomes we detected putative H/ACA sRNAs, in four Sulfolobales species and in Aeropyrum pernix, that might guide Psi 35 formation in pre-tRNA(Tyr)(GUA). This modification is achieved by Pus7p in eukarya. The validity of the computational predictions was verified by in vitro reconstitution of H/ACA sRNPs using the identified Sulfolobus solfataricus H/ACA sRNA. Comparison of Pus7-like enzymes encoded by archaeal genomes revealed amino acid substitutions in motifs IIIa and II in Sulfolobales and A. pernix Pus7-like enzymes. These conserved RNA:Psi-synthase- motifs are essential for catalysis. As expected, the recombinant Pyrococcus abyssi aPus7 was fully active and acted at positions 35 and 13 and other positions in tRNAs, while the recombinant S. solfataricus aPus7 was only found to have a poor activity at position 13. We showed that the presence of an A residue 3' to the target U residue is required for P. abyssi aPus7 activity, and that this is not the case for the reconstituted S. solfataricus H/ACA sRNP. In agreement with the possible formation of Psi 35 in tRNA(Tyr)(GUA) by aPus7 in P. abyssi and by an H/ACA sRNP in S. solfataricus, the A36G mutation in the P. abyssi tRNA(Tyr)(GUA) abolished Psi 35 formation when using P. abyssi extract, whereas the A36G substitution in the S. solfataricus pre-tRNA(Tyr) did not affect Psi 35 formation in this RNA when using an S. solfataricus extract.


Assuntos
Transferases Intramoleculares/química , RNA Arqueal/química , RNA Guia/química , RNA de Transferência de Tirosina/química , Sulfolobales/enzimologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Sequência de Bases , Transferases Intramoleculares/genética , Transferases Intramoleculares/metabolismo , Dados de Sequência Molecular , Pyrococcus abyssi/enzimologia , Precursores de RNA/química , Precursores de RNA/metabolismo , RNA Arqueal/metabolismo , RNA Nucleolar Pequeno/química , RNA de Transferência de Tirosina/metabolismo , Proteínas Recombinantes/metabolismo , Ribonucleoproteínas/metabolismo , Sulfolobales/genética , Sulfolobus solfataricus/enzimologia
14.
Appl Environ Microbiol ; 74(4): 942-9, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18083851

RESUMO

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 degrees 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 degrees 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 degrees 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.


Assuntos
Fontes Termais/microbiologia , Ferro/metabolismo , Filogenia , Sulfolobales/genética , Sequência de Bases , Análise por Conglomerados , Primers do DNA/genética , Concentração de Íons de Hidrogênio , Hibridização in Situ Fluorescente , Microscopia Eletrônica de Transmissão , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Homologia de Sequência , Sulfatos/metabolismo , Sulfolobales/crescimento & desenvolvimento , Sulfolobales/metabolismo , Sulfolobales/ultraestrutura , Temperatura , Wyoming
15.
Environ Microbiol ; 8(11): 2050-6, 2006 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-17014503

RESUMO

This study used a culture-independent molecular approach to investigate the archaeal community composition of thermophilic bioleaching reactors. Two culture samples, MTC-A and MTC-B, grown with different concentrations of chalcopyrite (CuFeS2), a copper sulfidic ore, at a temperature of 78 degrees C and pH 1.6 were studied. Phylogenetic analysis of the 16S rRNA genes revealed that both cultures consisted of Archaea belonging to the Sulfolobales. The 16S rRNA gene clone library of MTC-A grown with 4% (w/v) chalcopyrite was dominated by a unique phylotype related to Sulfolobus shibatae (69% of total clones). The remaining clones were affiliated with Stygiolobus azoricus (11%), Metallosphaera sp. J1 (8%), Acidianus infernus (2%), and a novel phylotype related to Sulfurisphaera ohwakuensis (10%). In contrast, the clones from MTC-B grown with 12% (w/v) chalcopyrite did not appear to contain Sulfolobus shibatae-like organisms. Instead the bioleaching consortium was dominated by clones related to Sulfurisphaera ohwakuensis (73.9% of total clones). The remaining microorganisms detected were similar to those found in MTC-A.


Assuntos
Reatores Biológicos/microbiologia , Cobre/metabolismo , Sulfolobales/classificação , Biodiversidade , Genes de RNAr , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfolobales/genética , Sulfolobales/isolamento & purificação
16.
Genome Biol ; 5(3): R17, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15003120

RESUMO

BACKGROUND: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively). RESULTS: Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus. CONCLUSIONS: We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.


Assuntos
Archaea/genética , Proteínas Arqueais/fisiologia , Filogenia , Biossíntese de Proteínas/fisiologia , Transcrição Genética/fisiologia , Archaea/enzimologia , Proteínas Arqueais/genética , DNA Arqueal/genética , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/fisiologia , Bases de Dados Genéticas , Euryarchaeota/genética , Evolução Molecular , Transferência Genética Horizontal/genética , Genes Arqueais/genética , Genoma Arqueal , Mathanococcus/enzimologia , Mathanococcus/genética , Biossíntese de Proteínas/genética , Sulfolobales/enzimologia , Sulfolobales/genética , Thermoplasmales/enzimologia , Thermoplasmales/genética , Transcrição Genética/genética
17.
Extremophiles ; 5(4): 241-5, 2001 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-11523893

RESUMO

A spherical thermoacidophilic archaeon, strain TA-2, was obtained from acidic hot springs located in Ohwaku Valley, Hakone, Japan. This isolate is an obligate aerobic chemoorganoheterotroph that grows optimally at about 75 degrees C, pH 2.8. The G + C content of DNA from TA-2 is 47 mol%. The 16S rRNA gene from TA-2 showed more than 99% similarity with those of Metallosphaera sedula and Metallosphaera prunae and less than 92% similarity with other members of the order Sulfolobales. DNA-DNA hybridization experiments showed more than 93% genomic DNA homology among TA-2, M. sedula DSM5348T, and M. prunae DSM10039T. However, TA-2 lacks calditoglycerocaldarchaeol derivatives, which are usually found in the membrane lipids of members of the order Sulfolobales. Therefore, calditoglycerocaldarchaeol may not be essential for survival in thermophilic and acidophilic environments. The isolate was deposited as Metallosphaera sedula TA-2 (JCM 9064, IFO 15160).


Assuntos
Sulfolobales , Adaptação Biológica , Diglicerídeos/genética , Deleção de Genes , Glicolipídeos/genética , Sulfolobales/genética , Sulfolobales/crescimento & desenvolvimento , Sulfolobales/metabolismo , Temperatura
18.
Wei Sheng Wu Xue Bao ; 41(3): 259-64, 2001 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-12549077

RESUMO

The further study on thermoacidophilic archaea strain S5, with has been identified as Sulfosphaerellus thermoacidophilum gen.nov.,sp.nov, has shown it was able to grow facultatively aerobically by means of two sulfur-metabolizing modes of chemolithotrophy which is the characteristic of Acidianus. And the 16SrRNA gene of strain S5 was amplified, cloned and sequenced, a phylogenetic tree was constructed on the 16SrRNA gene sequences. The tree clearly indicated that strain S5 formed the same lineage with Acidianus brierleyi. Thus strain S5 should be the member of Acidianus. However, there are only 44%, 22% and 23% genomic DNA similarity between S5 and A. brierleyi. A. infernus and A. ambivalens, respectively. And the G + C content of S5 DNA is 38%, which is 5% ~ 7% higher than the reported G + C contents of the other Acidianus species (31% or 32.7%) . In addition, strain S5 is a strictly chemolithoautotrophs, which is obviously different from facultative chemolithotrophs of A brierleyi. Based on the observed differences, strain S5 represents a new species within the genus Acidianus. A new species name, Acidianus tengchongenses, was proposed for it. The type strain is designated S5.


Assuntos
Acidianus/classificação , DNA Arqueal/genética , RNA Ribossômico 16S/genética , Sulfolobales/classificação , Terminologia como Assunto , Acidianus/genética , Acidianus/isolamento & purificação , Acidianus/ultraestrutura , Sequência de Bases , Fontes Termais/microbiologia , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Sulfolobales/genética , Sulfolobales/isolamento & purificação , Microbiologia da Água
19.
FEMS Microbiol Lett ; 170(1): 31-9, 1999 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-9919650

RESUMO

The distribution of the alcohol dehydrogenase gene (adh) among different Archaea was investigated by Southern blot analysis revealing the potentiality of the adh gene as a specific marker for the genus Sulfolobus. Moreover, the in vivo expression of the adh gene from a new isolate of Sulfolobus solfataricus, G theta, was studied to investigate gene regulation in Archaea. Primer extension analysis allowed the identification of a single initiation site and the TATA box element. Comparison of the G theta adh promoter with the corresponding Ssadh (adh from S. solfataricus) and RC3adh (adh from Sulfolobus RC3) also revealed the presence of two putative regulatory inverted repeats at the 5' of the TATA element. Northern blot analysis and enzymatic assays demonstrated that the transcription and expression of the G theta adh gene is regulated by different carbon and energy sources or by the natural substrate of the ADH enzyme.


Assuntos
Álcool Desidrogenase/genética , DNA Arqueal/análise , Genes Arqueais , Sulfolobales/enzimologia , Sulfolobales/genética , Álcool Desidrogenase/metabolismo , Sequência de Bases , Southern Blotting , Meios de Cultura , Regulação da Expressão Gênica em Archaea , Genótipo , Dados de Sequência Molecular , Regiões Promotoras Genéticas , RNA Arqueal/genética , RNA Mensageiro/genética , Especificidade por Substrato , Sulfolobales/crescimento & desenvolvimento , Transcrição Genética
20.
Int J Syst Bacteriol ; 48 Pt 2: 451-6, 1998 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-9731283

RESUMO

Three spherical thermoacidophilic archaea (strains TA-1T, TA-13, TA-14) were obtained from acidic hot springs located in Ohwaku Valley, Hakone, Japan. All the isolates are facultatively anaerobic, and grew optimally at around 85 degrees C, pH 2.0. Isolate TA-1T was characterized further. The G + C content of DNA from TA-1T is 33 mol%. Although these properties resemble those of the genus Acidianus, the sequence of the 16S rRNA gene from strain TA-1T was more similar to that of species of Stygiolobus than of Acidianus. DNA-DNA hybridization experiments also indicated that strain TA-1T is clearly distinguished phylogenetically from the members of Acidianus, Sulfolobus and Metallosphaera. On the basis of the distinct physiological and molecular properties, we describe the new strains as members of the new genus Sulfurisphaera. The type species of the genus is Sulfurisphaera ohwakuensis, and the type strain of the species is TA-1T (= IFO 15161T).


Assuntos
Sulfolobales/classificação , Composição de Bases , Sequência de Bases , DNA Bacteriano , Água Doce/microbiologia , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Filogenia , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Sulfolobales/genética , Sulfolobales/ultraestrutura
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