Thermomicrobium roseum
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ABSTRACT:
PROVIDER: PRJNA32631 | ENA |
REPOSITORIES: ENA
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Project description:Obligate thermophile with unusual cell wall structure.
| PRJNA32569 | ENA
Project description:In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.
| S-EPMC2615216 | biostudies-literature
Project description:Transaminases catalyze the reversible transfer reaction of an amino group between a primary amine and an α-keto acid, utilizing pyridoxal 5'-phosphate as a cofactor. ω-transaminases (ωTAs) recognize an amino group linked to a non-α carbon of amine substrates. Recently, a novel (S)-enantioselective ωTA from Thermomicrobium roseum (Tr-ωTA) was identified and its enzymatic activity reported. However, the detailed mechanism of (S)-enantioselective substrate recognition remained unclear. In this study, we determined the crystal structure of Tr-ωTA at 1.8 Å resolution to elucidate the mechanism underlying Tr-ωTA substrate (S)-enantioselectivity. A structural analysis of Tr-ωTA along with molecular docking simulations revealed that two pockets at the active site tightly restrict the size and orientation of functional groups of substrate candidates. Based on the structural information and docking simulation results, we propose a comprehensive catalytic mechanism of Tr-ωTA. The present study thus provides structural and functional insights into the (S)-enantioselectivity of Tr-ωTA.
| S-EPMC6502798 | biostudies-literature
Project description:Methanogenic archaeon with unusual filamentous structure
| PRJNA13015 | ENA
Project description:Division and degradation of bacterial cell walls requires coordinated action of a myriad of enzymes. This particularly applies to the elaborate cell walls of acid-fast organisms such as Mycobacterium tuberculosis, which consist of a multi-layered cell wall that contains an unusual glycan called arabinogalactan. Enzymes that cleave the D-arabinan core of this structure have not previously been identified in any organism. We have interrogated the diverse carbohydrate degrading enzymes expressed by the human gut microbiota and uncovered four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using novel exo-D-galactofuranosidases from gut bacteria we generated enriched D-arabinan and used it to identify Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo- acting enzymes that cleave D-arabinan. We have identified new members of the DUF2961 family (GH172), and a novel family of glycoside hydrolases (DUF4185) that display endo-ᴅ-arabinofuranase activity. The DUF4185 enzymes are conserved in mycobacteria and found in many microbes, suggesting that the ability to cleave these mycobacterial glycans plays an important role in the biology of diverse organisms. All mycobacteria encode two conserved endo-D-arabinanases that display different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.
2023-03-24 | PXD039984 | Pride
Project description:An obligate commensal thermophile requiring a co-culture to provide certain metabolites.
| PRJNA12994 | ENA
Project description:An obligate commensal thermophile requiring a co-culture to provide certain metabolites
| PRJNA15726 | ENA
Project description:This study utilized the thermophile Thermus scotoductus SA-01 to determine changes in gene expression based on growth with convective or dielectric microwave heating (2.45 GHz) at 65°C. A total of 344 genes were identified as significantly differentially regulated across the three time points. Our results reveal that a large number of genes involved in cell wall recycling and biogenesis were induced, corroborating the elongated cell morphology observed in cells grown with dielectric heating. Genes associated with sugar metabolism were induced across multiple time points, while genes involved in denitrification were repressed, suggesting the different modes of heating influence metabolism. Additionally, an unexpected link was observed with regards to enzymes in which molybdenum serves as a co-factor.
2016-08-29 | GSE79201 | GEO