Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan

Sakai, Hiroyuki D.; Kurosawa, Norio

doi:10.1186/s13104-019-4488-5

Cited by 10 publications

(6 citation statements)

References 33 publications

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“…More recently, biochemical properties of the B-family polymerases of Sulfolobus and related genera have been investigated, and argue that the PolB1 enzymes play this replicative role ( Choi et al, 2011 ; Bauer et al, 2012 ; Peng et al, 2016 ; Yan et al, 2017 ), and this conclusion is supported by functional genetic criteria in S. acidocaldarius (this study) and closely related crenarchaea ( Feng et al, 2020 ). The recent evidence that Sulfodiicoccus acidiphilus , a member of the order Sulfolobales lacks PolB3 ( Sakai and Kurosawa, 2019 ) also strongly supports a replicative role of PolB1.…”

Section: Discussionmentioning

confidence: 91%

PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

et al. 2020

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The thermophilic crenarchaeon Sulfolobus acidocaldarius has four DNA polymerases (DNAPs): PolB1, PolB2, PolB3, and Dbh (PolY). Previous in vitro studies suggested that PolB1 is the main replicative DNAP of Sulfolobales whereas PolB2 and Y-family polymerases Dpo4 (Saccharolobus solfataricus) or Dbh are involved in DNA repair and translesion DNA synthesis. On the other hand, there are various opinions about the role of PolB3, which remains to be clearly resolved. In order to examine the roles of the DNAPs of S. acidocaldarius through in vivo experiments, we constructed polB2, polB3, and dbh deletion strains and characterized their phenotypes. Efforts to construct a polB1 deletion strain were not successful; in contrast, it was possible to isolate triple gene-deletion strains lacking polB2, polB3, and dbh. The growth of these strains was nearly the same as that of the parent strains under normal growth conditions. The polB2, polB3, and dbh single-deletion strains were sensitive to some types of DNA-damaging treatments, but exhibited normal sensitivity to UV irradiation and several other damaging treatments. Overall, the genotype which exhibited the greatest sensitivity to the DNA-damaging treatments we tested was the ΔpolB2 ΔpolB3 combination, providing the first evidence of overlapping function for these two DNAPs in vivo. The results of our study strongly suggest that PolB1 is responsible for the DNA replication of both the leading and lagging strands and is sufficient to complete the repair of most DNA damage under normal growth conditions in S. acidocaldarius.

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Section: Discussionmentioning

confidence: 91%

PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

et al. 2020

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“…37a). The member species metabolized carbohydrates and amino acids [145,146] into pyruvate and CO2(g). The organisms further fermented pyruvate into lactate and CO2(g).…”

Section: )mentioning

confidence: 99%

Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya

Muturi

Muthui

Njogu

et al. 2020

Preprint

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The obstacle to optimal utilization of biogas technology is poor understanding of biogas' microbiome diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversities studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria richness dominated and composed 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, fungi and Archaea composed 5 phyla, the fungi were richer; suggesting importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Synergistales to mention but few, also catabolized macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulated PH2 and reduced metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, conveying largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas' microbiomes over wide environmental conditions and its productivity provides insights into better management and other effective strategies that ameliorate existing biochemical issues.

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“…One of the main obstacles to better understanding the world of the Sulfolobales has been the difficulty associated with de novo sequencing of species without guiding reference sequences and with plentiful repetitive roadblocks (from transposable elements and CRISPR arrays). While some closed genomes have been reported (She et al ., 2001; Chen et al ., 2005; Auernik et al ., 2008), recent efforts have considerably expanded the genomic repository for the order (Dai et al ., 2016; Urbieta et al ., 2017; Counts et al ., 2018; Sakai and Kurosawa, 2019). Ongoing efforts focus on new isolates (‘ Candidatus Acidianus copahuensis ’ (Urbieta et al ., 2014), Sulfodiicoccus acidiphilus (Sakai and Kurosawa, 2019), ‘ Metallosphaera yellowstonensis ’ (Kozubal et al ., 2011), Sulfuracidifex tepidarius (Itoh et al ., 2020) and Sulfolobus sp.…”

Section: Introductionmentioning

confidence: 99%

Life in hot acid: a genome‐based reassessment of the archaeal order Sulfolobales

Counts

Willard

Kelly

2020

Environmental Microbiology

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The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65 C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic reorganization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.

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Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan

Cited by 10 publications

References 33 publications

PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya

Life in hot acid: a genome‐based reassessment of the archaeal order Sulfolobales

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