scholarly journals Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism

2021 ◽  
Vol 10 (1) ◽  
pp. 60
Author(s):  
Stéven Yvenou ◽  
Maxime Allioux ◽  
Alexander Slobodkin ◽  
Galina Slobodkina ◽  
Mohamed Jebbar ◽  
...  
Keyword(s):  
Elemental Sulfur ◽  
Co2 Assimilation ◽  
Dissimilatory Sulfate Reduction ◽  
Base Pairs ◽  
Thermophilic Microorganism ◽  
Circular Chromosome ◽  
Sulfur Disproportionation ◽  
Genetic Potential ◽  
Large Panel ◽  
Poorly Soluble

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S0-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO2 assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68T is conserved in the genomes of a large panel of other S0-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S0 is poorly soluble and unable to cross the cytoplasmic membrane in this form.

scholarly journals Microhomology Selection for Microhomology Mediated End Joining in Saccharomyces cerevisiae

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 284 ◽  
Author(s):  
Kihoon Lee ◽  
Jae-Hoon Ji ◽  
Kihoon Yoon ◽  
Jun Che ◽  
Ja-Hwan Seol ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Budding Yeast ◽  
Product Formation ◽  
Dna Breaks ◽  
End Joining ◽  
Base Pairs ◽  
Circular Chromosome ◽  
Proximal Side ◽  
Selection For ◽  
Insight Into

Microhomology-mediated end joining (MMEJ) anneals short, imperfect microhomologies flanking DNA breaks, producing repair products with deletions in a Ku- and RAD52-independent fashion. Puzzlingly, MMEJ preferentially selects certain microhomologies over others, even when multiple microhomologies are available. To define rules and parameters for microhomology selection, we altered the length, the position, and the level of mismatches to the microhomologies flanking homothallic switching (HO) endonuclease-induced breaks and assessed their effect on MMEJ frequency and the types of repair product formation. We found that microhomology of eight to 20 base pairs carrying no more than 20% mismatches efficiently induced MMEJ. Deletion of MSH6 did not impact MMEJ frequency. MMEJ preferentially chose a microhomology pair that was more proximal from the break. Interestingly, MMEJ events preferentially retained the centromere proximal side of the HO break, while the sequences proximal to the telomere were frequently deleted. The asymmetry in the deletional profile among MMEJ products was reduced when HO was induced on the circular chromosome. The results provide insight into how cells search and select microhomologies for MMEJ in budding yeast.

scholarly journals Groundwater cable bacteria conserve energy by sulfur disproportionation

2019 ◽  
Vol 14 (2) ◽  
pp. 623-634 ◽  
Author(s):  
Hubert Müller ◽  
Sviatlana Marozava ◽  
Alexander J. Probst ◽  
Rainer U. Meckenstock
Keyword(s):  
16S Rrna ◽  
Electron Donor ◽  
Nitrate Reduction ◽  
Elemental Sulfur ◽  
Single Cells ◽  
Sulfur Oxidation ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Long Distance ◽  
Sulfur Disproportionation

AbstractCable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.

scholarly journals Genome Sequence Analysis of the Emerging Human Pathogenic Acetic Acid Bacterium Granulibacter bethesdensis

2007 ◽  
Vol 189 (23) ◽  
pp. 8727-8736 ◽  
Author(s):  
David E. Greenberg ◽  
Stephen F. Porcella ◽  
Adrian M. Zelazny ◽  
Kimmo Virtaneva ◽  
Dan E. Sturdevant ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Sequence Similarity ◽  
Gluconobacter Oxydans ◽  
Acetic Acid Bacterium ◽  
Open Reading Frames ◽  
Dna Uptake ◽  
Base Pairs ◽  
Circular Chromosome ◽  
Susceptibility To Infection ◽  
Bacteria And Fungi

ABSTRACT Chronic granulomatous disease (CGD) is an inherited immune deficiency characterized by increased susceptibility to infection with Staphylococcus, certain gram-negative bacteria, and fungi. Granulibacter bethesdensis, a newly described genus and species within the family Acetobacteraceae, was recently isolated from four CGD patients residing in geographically distinct locales who presented with fever and lymphadenitis. We sequenced the genome of the reference strain of Granulibacter bethesdensis, which was isolated from lymph nodes of the original patient. The genome contains 2,708,355 base pairs in a single circular chromosome, in which 2,437 putative open reading frames (ORFs) were identified, 1,470 of which share sequence similarity with ORFs in the nonpathogenic but related Gluconobacter oxydans genome. Included in the 967 ORFs that are unique to G. bethesdensis are ORFs potentially important for virulence, adherence, DNA uptake, and methanol utilization. GC% values and best BLAST analysis suggested that some of these unique ORFs were recently acquired. Comparison of G. bethesdensis to other known CGD pathogens demonstrated conservation of some putative virulence factors, suggesting possible common mechanisms involved in pathogenesis in CGD. Genotyping of the four patient isolates by use of a custom microarray demonstrated genome-wide variations in regions encoding DNA uptake systems and transcriptional regulators and in hypothetical ORFs. G. bethesdensis is a genetically diverse emerging human pathogen that may have recently acquired virulence factors new to this family of organisms.

Elemental Sulfur Disproportionation in the Redox Condensation Reaction betweeno-Halonitrobenzenes and Benzylamines

2014 ◽  
Vol 126 (50) ◽  
pp. 14028-14032 ◽  
Author(s):  
Thanh Binh Nguyen ◽  
Ludmila Ermolenko ◽  
Pascal Retailleau ◽  
Ali Al-Mourabit
Keyword(s):  
Elemental Sulfur ◽  
Condensation Reaction ◽  
Sulfur Disproportionation

ChemInform Abstract: Elemental Sulfur Disproportionation in the Redox Condensation Reaction Between o-Halonitrobenzenes and Benzylamines.

ChemInform ◽  
2015 ◽  
Vol 46 (19) ◽  
pp. no-no
Author(s):  
Thanh Binh Nguyen ◽  
Ludmila Ermolenko ◽  
Pascal Retailleau ◽  
Ali Al-Mourabit
Keyword(s):  
Elemental Sulfur ◽  
Condensation Reaction ◽  
Sulfur Disproportionation

A chemoautotrophic and thermophilic microorganism isolated from an acid hot spring

1973 ◽  
Vol 19 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Corale L. Brierley ◽  
James A. Brierley
Keyword(s):  
Heat Resistance ◽  
Respiration Rate ◽  
Base Composition ◽  
Elemental Sulfur ◽  
Hot Spring ◽  
Amorphous Layer ◽  
Maximum Temperature ◽  
Dna Base Composition ◽  
Thermophilic Microorganism ◽  
Dna Base

A pleomorphic, acidophilic, and chemoautotrophic microbe is described. The cell is bound by a membrane and a diffuse, amorphous layer. The isolate used either sulfur or iron as a source of energy. Morphological and nutritional similarities as well as corresponding thermophilic and acidophilic requirements suggest a relationship to Sulfolobus. The organism tolerates 80 °C for longer than 2 h, but heat resistance is not attributed to a bacterial spore. The maximum temperature for growth is 70 °C; the minimum about 45 °C.The DNA base composition is 57 ± 3 mole % GC. Yeast extract enhances growth of the isolate on iron and sulfur substrates, but does not significantly enhance the isolate's respiration rate on these same substrates.The isolate requires induction by sulfur or iron for maximum respiration on these substrates, respectively. Optimum oxidation of elemental sulfur occurred at pH 2.0 and gave a [Formula: see text] of 163; oxidation on iron gave a maximum [Formula: see text] of 879.

scholarly journals Whole Genome Sequence of biosurfactant producing Bacillus tequilensis

2020 ◽  
Author(s):  
Anuraj Nayarisseri ◽  
Sanjeev Kumar Singh
Keyword(s):  
Genome Sequence ◽  
Variant Calling ◽  
Whole Genome Sequence ◽  
Bacillus Species ◽  
Trna Genes ◽  
Whole Genome ◽  
Base Pairs ◽  
Circular Chromosome ◽  
Protein Encoding ◽  
Bacillus Tequilensis

Abstract We announce the complete genome sequence of Bacillus tequilensis, a biosurfactant producing bacterium isolated from Chilika lake, Odisha, India(latitude and longitude: 19.8450 N 85.4788 E). The genome sequence is 4.47 MB consisting of 4,478,749 base pairs forming a circular chromosome with 528 scaffolds, 4492 protein-encoding genes(ORFs), 81 tRNA genes, and 114 ribosomal RNA transcription units. The total number of raw reads was 4209415 and processed reads were 4058238 with predicted genes of 4492. The whole-genome obtained from the present investigation was used for genome annotation, variant calling, variant annotation and comparative genome analysis with other existing Bacillus species. In this study we constructed a pathway which describe the biosurfactant metabolism of Bacillus tequilensis and identified the genes such as SrfAD, SrfAC, SrfAA which are involved in biosurfactant synthesis. The sequence of the same was deposited in Genbank database with accession MUG02427.1, MUG02428.1, MUG02429.1, MUG03515.1 respectively. The whole-genome sequence was submitted to Genbank with an accession RMVO00000000 and the raw reads can be obtained from SRA, NCBI repository using accession: SRX5023292.

Elemental Sulfur Disproportionation in the Redox Condensation Reaction betweeno-Halonitrobenzenes and Benzylamines

2014 ◽  
Vol 53 (50) ◽  
pp. 13808-13812 ◽  
Author(s):  
Thanh Binh Nguyen ◽  
Ludmila Ermolenko ◽  
Pascal Retailleau ◽  
Ali Al-Mourabit
Keyword(s):  
Elemental Sulfur ◽  
Condensation Reaction ◽  
Sulfur Disproportionation

scholarly journals Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil

2020 ◽  
Vol 70 (3) ◽  
pp. 1489-1495 ◽  
Author(s):  
Xiao-Tian Quan ◽  
Muhammad Zubair Siddiqi ◽  
Qing-Zhen Liu ◽  
Sang-Mi Lee ◽  
Wan-Taek Im
Keyword(s):  
Type Species ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Base Pairs ◽  
Circular Chromosome ◽  
Content Type ◽  
Link Type ◽  
Ginseng Cultivation

A Gram-stain-negative, strictly aerobic, motile, ivory-coloured and rod-shaped bacterium (designated Gsoil 520T) isolated from ginseng cultivation soil was characterized by using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 520T was observed to grow optimally at 30 °C and pH 7.0 on Reasoner's 2A agar medium. The results of phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that Gsoil 520T belongs to the genus Devosia of the family Hyphomicrobiaceae and was most closely related to Devosia epidermidihirudinis E84T (98.0 %), Devosia yakushimensis Yak96BT (97.7 %), Devosia neptuniae J1T (97.7 %) and Devosia chinhatensis IPL18T (96.8 %). The complete genome of strain Gsoil 520T is a presumptive circular chromosome of 4 480 314 base pairs having G+C content of 63.7 mol%. A total of 4 354 genes, 4 303 CDS and 43 rRNA genes were assigned a putative function. The major isoprenoid quinone was Q-10. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids (AL1 and AL3). The predominant fatty acids of strain Gsoil 520T were C18 : 1ω7c 11-methyl, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c (summed feature 8) supporting the affiliation of strain Gsoil 520T to the genus Devosia . The low values of DNA–DNA hybridization distinguished strain Gsoil 520T from the recognized species of the genus Devosia . Thus, the novel isolate represents a novel species of the genus Devosia , for which the name Devosia ginsengisoli sp. nov. is proposed, with the type strain Gsoil 520T (=KACC 19440T=LMG 30329T).

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