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Keywords = colorless filamentous bacteria

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24 pages, 4840 KiB  
Article
Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis, Where Persulfide Dioxygenase Plays a Key Role
by Tatyana S. Rudenko, Liubov I. Trubitsina, Vasily V. Terentyev, Ivan V. Trubitsin, Valentin I. Borshchevskiy, Svetlana V. Tishchenko, Azat G. Gabdulkhakov, Alexey A. Leontievsky and Margarita Yu. Grabovich
Int. J. Mol. Sci. 2024, 25(20), 10962; https://doi.org/10.3390/ijms252010962 - 11 Oct 2024
Cited by 1 | Viewed by 1496
Abstract
Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa [...] Read more.
Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa representatives. Annotation of the genome of Beggiatoa leptomitoformis D-402 did not identify any genes for the oxidation or reduction of elemental sulfur. By searching BLASTP, two putative persulfide dioxygenase (PDO) homologs were found in the genome of B. leptomitoformis. In some heterotrophic prokaryotes, PDO is involved in the oxidation of sulfane sulfur. According to HPLC-MS/MS, the revealed protein was reliably detected in a culture sample grown only in the presence of endogenous sulfur and CO2. The recombinant protein from B. leptomitoformis was active in the presence of glutathione persulfide. The crystal structure of recombinant PDO exhibited consistency with known structures of type I PDO. Thus, it was shown that B. leptomitoformis uses PDO to oxidize endogenous sulfur. Additionally, on the basis of HPLC-MS/MS, RT-qPCR, and the study of PDO reaction products, we predicted the interrelation of PDO and Sox-system function in the oxidation of endogenous sulfur in B. leptomitoformis and the connection of this process with energy metabolism. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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19 pages, 15110 KiB  
Article
Phylogeny and Metabolic Potential of New Giant Sulfur Bacteria of the Family Beggiatoaceae from Coastal-Marine Sulfur Mats of the White Sea
by Nikolai V. Ravin, Tatyana S. Rudenko, Alexey V. Beletsky, Dmitry D. Smolyakov, Andrey V. Mardanov, Margarita Yu. Grabovich and Maria S. Muntyan
Int. J. Mol. Sci. 2024, 25(11), 6028; https://doi.org/10.3390/ijms25116028 - 30 May 2024
Cited by 1 | Viewed by 1645
Abstract
The family Beggiatoaceae is currently represented by 25 genera in the Genome Taxonomy Database, of which only 6 have a definite taxonomic status. Two metagenome-assembled genomes (MAGs), WS_Bin1 and WS_Bin3, were assembled from metagenomes of the sulfur mats coating laminaria remnants in the [...] Read more.
The family Beggiatoaceae is currently represented by 25 genera in the Genome Taxonomy Database, of which only 6 have a definite taxonomic status. Two metagenome-assembled genomes (MAGs), WS_Bin1 and WS_Bin3, were assembled from metagenomes of the sulfur mats coating laminaria remnants in the White Sea. Using the obtained MAGs, we first applied phylogenetic analysis based on whole-genome sequences to address the systematics of Beggiatoaceae, which clarify the taxonomy of this family. According to the average nucleotide identity (ANI) and average amino acid identity (AAI) values, MAG WS_Bin3 was assigned to a new genus and a new species in the family Beggiatoaceae, namely, ‘Candidatus Albibeggiatoa psychrophila’ gen. nov., sp. nov., thus providing the revised taxonomic status of the candidate genus ‘BB20’. Analysis of 16S rRNA gene homology allowed us to identify MAG WS_Bin1 as the only currently described species of the genus ‘Candidatus Parabeggiatoa’, namely, ‘Candidatus Parabeggiatoa communis’, and consequently assign the candidate genus ‘UBA10656’, including four new species, to the genus ‘Ca. Parabeggiatoa’. Using comparative whole-genome analysis of the members of the genera ‘Candidatus Albibeggiatoa’ and ‘Ca. Parabeggiatoa’, we expanded information on the central pathways of carbon, sulfur and nitrogen metabolism in the family Beggiatoaceae. Full article
(This article belongs to the Section Molecular Biology)
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11 pages, 4570 KiB  
Article
tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix
by Nikolai V. Ravin, Dmitry D. Smolyakov, Nikita D. Markov, Alexey V. Beletsky, Andrey V. Mardanov, Tatyana S. Rudenko and Margarita Yu. Grabovich
Microorganisms 2023, 11(10), 2521; https://doi.org/10.3390/microorganisms11102521 - 9 Oct 2023
Cited by 2 | Viewed by 1777
Abstract
Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the [...] Read more.
Currently, the phylogeny of the genus Thiothrix is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus Thiothrix. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (tilS) and the β subunit of RNA polymerase (rpoB) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus Thiothrix. The genomes of Thiothrix strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the tilS gene consistently showed that MK1 and WS belong to Thiothrix lacustris, while DNT52, DNT53, and H33 belong to Thiothrix subterranea. The tilS gene fragments were subjected to high-throughput sequencing to profile the Thiothrix mat of a sulfidic spring, which revealed the presence of known species of Thiothrix and new species-level phylotypes. Thus, the use of tilS and rpoB as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus Thiothrix. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential)
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19 pages, 10381 KiB  
Article
Metagenomics Revealed a New Genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. and a New Species ‘Candidatus Thiothrix putei’ sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics
by Nikolai V. Ravin, Maria S. Muntyan, Dmitry D. Smolyakov, Tatyana S. Rudenko, Alexey V. Beletsky, Andrey V. Mardanov and Margarita Yu. Grabovich
Int. J. Mol. Sci. 2023, 24(18), 14199; https://doi.org/10.3390/ijms241814199 - 17 Sep 2023
Cited by 3 | Viewed by 2166
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG [...] Read more.
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%). We proposed to assign GKL-01 to a new species and genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name ‘Candidatus Thiothrix putei’ sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically. Full article
(This article belongs to the Special Issue Advances in Gene Research in Nuclear-Free Organisms and Entities: Prokaryotes and Organelles)
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11 pages, 1793 KiB  
Article
Comparative Genomics of Beggiatoa leptomitoformis Strains D-401 and D-402T with Contrasting Physiology But Extremely High Level of Genomic Identity
by Tatyana S. Rudenko, Sergey V. Tarlachkov, Nikolay D. Shatskiy and Margarita Yu. Grabovich
Microorganisms 2020, 8(6), 928; https://doi.org/10.3390/microorganisms8060928 - 19 Jun 2020
Cited by 3 | Viewed by 4642
Abstract
Representatives of filamentous colorless sulfur-oxidizing bacteria often dominate in sulfide biotopes, preventing the diffusion of toxic sulfide into the water column. One of the most intriguing groups is a recently described Beggiatoa leptomitoformis including strains D-401 and D-402T. Both strains have [...] Read more.
Representatives of filamentous colorless sulfur-oxidizing bacteria often dominate in sulfide biotopes, preventing the diffusion of toxic sulfide into the water column. One of the most intriguing groups is a recently described Beggiatoa leptomitoformis including strains D-401 and D-402T. Both strains have identical genes encoding enzymes which are involved in the oxidation of hydrogen sulfide and thiosulfate. Surprisingly, the B. leptomitoformis strain D-401 is not capable to grow lithotrophically in the presence of reduced sulfur compounds and to accumulate elemental sulfur inside the cells, in contrast to the D-402T strain. In general, genomes of D-401 and D-402T have an extremely high level of identity and only differ in 1 single-letter substitution, 4 single-letter indels, and 16 long inserts. Among long inserts, 14 are transposons. It was shown that in the D-401 strain, a gene coding for a sulfur globule protein was disrupted by one of the mentioned transposons. Based on comparative genomics, RT-qPCR, and HPLC-MS/MS, we can conclude that this gene plays a crucial role in the formation of the sulfur globules inside the cells, and the disruption of its function prevents lithotrophic growth of B. leptomitoformis in the presence of reduced sulfur compounds. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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