Extremophile organisms
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Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.
- Publikační typ
- časopisecké články MeSH
Biologická evoluce některých živých organismů by mohla přinést nový vhled do etiologie stárnutí. Organismy schopné odolat extrémním podmínkám jsou příklady dokonalé evoluce z hlediska biologické odolnosti: jejich genetická adaptace selekcí pomohla přeměnit nepřátelské prostředí na prostředí optimální. Když jsou extremofilní organismy Deinococcus radiodurans nebo Arthrobacter agilis vystaveny radiaci, mohou přejít ze stavu "klinické smrti" do procesu tzv. "vzkříšení" prostřednictvím sebeopravy. Bylo prokázáno, že stárnutí a nemoci související s věkem (ARD) sdílejí společnou hlavní příčinu: degradaci a poškození proteinů. Zejména karbonylované proteiny lze považovat za markery a akcelerátory stárnutí a ARD a to včetně Alzheimerovy a Parkinsonovy choroby, cukrovky, psoriázy a rakoviny kůže. Současný výzkum je velmi slibný a může otevřít nové terapeutické přístupy a perspektivy se zaměřením na ochranu proteomu.
The biological evolution of some living organisms is opening up a new path: understanding why and how we age. Organisms capable of withstanding extreme conditions are examples of perfect evolution in terms of biological robustness: their genetic adaptation by selection has helped transform a hostile environment into an optimal environment. When the extremophiles such as Deinococcus radiodurans or Arthrobacter agilis bacterias are exposed to radiation, they can transition from a "clinical death" state to a "resurrection" process through self-repair. It has been shown that ageing and age-related diseases (ARD) share the same cause: protein damage. Especially, protein carbonylation can be considered as marker and accelerator of ageing and it is common marker of most ARD including Alzheimer and Parkinson diseases, diabetes, psoriasis, and skin cancer. Current research is promising and may open new therapeutic approaches and perspectives by targeting proteome protection.
- MeSH
- dlouhověkost * fyziologie MeSH
- karbonylace proteinů fyziologie MeSH
- lidé MeSH
- molekulární chaperony fyziologie MeSH
- proteolýza MeSH
- proteom fyziologie MeSH
- stárnutí kůže * fyziologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
In the extremophile bacterium Deinococcus radiodurans, the outermost surface layer is tightly connected with the rest of the cell wall. This integrated organization provides a compact structure that shields the bacterium against environmental stresses. The fundamental unit of this surface layer (S-layer) is the S-layer deinoxanthin-binding complex (SDBC), which binds the carotenoid deinoxanthin and provides both, thermostability and UV radiation resistance. However, the structural organization of the SDBC awaits elucidation. Here, we report the isolation of the SDBC with a gentle procedure consisting of lysozyme treatment and solubilization with the nonionic detergent n-dodecyl-β-d-maltoside, which preserved both hydrophilic and hydrophobic components of the SDBC and allows the retention of several minor subunits. As observed by low-resolution single-particle analysis, we show that the complex possesses a porin-like structural organization, but is larger than other known porins. We also noted that the main SDBC component, the protein DR_2577, shares regions of similarity with known porins. Moreover, results from electrophysiological assays with membrane-reconstituted SDBC disclosed that it is a nonselective channel that has some peculiar gating properties, but also exhibits behavior typically observed in pore-forming proteins, such as porins and ionic transporters. The functional properties of this system and its porin-like organization provide information critical for understanding ion permeability through the outer cell surface of S-layer-carrying bacterial species.
- MeSH
- bakteriální proteiny chemie genetika MeSH
- buněčná membrána chemie MeSH
- buněčná stěna chemie MeSH
- Deinococcus chemie genetika MeSH
- karotenoidy chemie MeSH
- membránové glykoproteiny chemie MeSH
- multiproteinové komplexy chemie genetika MeSH
- poriny chemie MeSH
- vazba proteinů genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Fungi from extreme environments, including acidophilic ones, belong to biotechnologically most attractive organisms. They can serve as a source of enzymes and metabolites with potentially uncommon properties and may actively participate within bioremediation processes. In respect of their biotechnological potential, extremophilic fungi are mostly studied as individual species. Nevertheless, microorganisms rarely live separately and they form biofilms instead. Living in biofilms is the most successful life strategy on the Earth and the biofilm is the most abundant form of life in extreme environments including highly acidic ones. Compared to bacterial fraction, fungal part of acidophilic biofilms represents a largely unexplored source of organisms with possible use in biotechnology and especially data on biofilms of highly acidic soils are missing. The functioning of the biofilm results from interactions between organisms whose metabolic capabilities are efficiently combined. When we look on acidophilic fungi and their biotechnological potential we should take this fact into account as well. The practical problem to be resolved in connection with extensive studies of exploitable properties and abilities of acidophilic fungi is the methodology of isolation of strains from the nature. In this respect, novel isolation techniques should be developed.
The monomeric photosystem I-light-harvesting antenna complex I (PSI-LHCI) supercomplex from the extremophilic red alga Cyanidioschyzon merolae represents an intermediate evolutionary link between the cyanobacterial PSI reaction center and its green algal/higher plant counterpart. We show that the C. merolae PSI-LHCI supercomplex is characterized by robustness in various extreme conditions. By a combination of biochemical, spectroscopic, mass spectrometry, and electron microscopy/single particle analyses, we dissected three molecular mechanisms underlying the inherent robustness of the C. merolae PSI-LHCI supercomplex: (1) the accumulation of photoprotective zeaxanthin in the LHCI antenna and the PSI reaction center; (2) structural remodeling of the LHCI antenna and adjustment of the effective absorption cross section; and (3) dynamic readjustment of the stoichiometry of the two PSI-LHCI isomers and changes in the oligomeric state of the PSI-LHCI supercomplex, accompanied by dissociation of the PsaK core subunit. We show that the largest low light-treated C. merolae PSI-LHCI supercomplex can bind up to eight Lhcr antenna subunits, which are organized as two rows on the PsaF/PsaJ side of the core complex. Under our experimental conditions, we found no evidence of functional coupling of the phycobilisomes with the PSI-LHCI supercomplex purified from various light conditions, suggesting that the putative association of this antenna with the PSI supercomplex is absent or may be lost during the purification procedure.
- MeSH
- biologická adaptace MeSH
- chlorofyl metabolismus MeSH
- cirkulární dichroismus MeSH
- fluorescenční spektrometrie MeSH
- fotosystém I (proteinový komplex) chemie metabolismus MeSH
- koncentrace vodíkových iontů MeSH
- molekulární evoluce MeSH
- Rhodophyta chemie fyziologie MeSH
- sinice chemie fyziologie MeSH
- světlo MeSH
- světlosběrné proteinové komplexy chemie metabolismus MeSH
- teplota MeSH
- zeaxanthiny metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Deep sequencing of prokaryotic 16S rDNA regularly reveals thousands of microbial species thriving in many common habitats. It is still unknown how this huge microbial diversity, including many potentially competing organisms, may persist at a single site. One of plausible hypotheses is that a large number of spatially separated microcommunities exist within each complex habitat. Smaller subset of the species may exist in each microcommunity and actually interact with each other. We sampled two groups of microbial stalactites growing at a single acidic mine drainage outlet as a model of multiplicated, low-complexity microhabitat. Samples from six other sites were added for comparison. Both tRFLP and 16S rDNA pyrosequencing showed that microbial communities containing 6 to 51 species-level operational taxonomic units (OTU) inhabited all stalactites. Interestingly, most OTUs including the highly abundant ones unpredictably alternated regardless of physical and environmental distance of the stalactites. As a result, the communities clustered independently on sample site and other variables when using both phylogenetic dissimilarity and OTU abundance metrics. Interestingly, artificial communities generated by pooling the biota of several adjacent stalactites together clustered by the locality more strongly than when the stalactites were analyzed separately. The most probable interpretation is that each stalactite contains likely random selection from the pool of plausible species. Such degree of stochasticity in assembly of extremophilic microbial communities is significantly greater than commonly proposed and requires caution when interpreting microbial diversity.
- MeSH
- Bacteria klasifikace izolace a purifikace metabolismus MeSH
- biodiverzita MeSH
- biofilmy MeSH
- DNA bakterií genetika MeSH
- druhová specificita MeSH
- fylogeneze * MeSH
- hornictví * MeSH
- kyseliny chemie MeSH
- mikrobiologie vody * MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- voda chemie MeSH
- Publikační typ
- časopisecké články MeSH
Haloalkane dehalogenases (EC 3.8.1.5, HLDs) are α/β-hydrolases which act to cleave carbon-halogen bonds. Due to their unique catalytic mechanism, broad substrate specificity and high robustness, the members of this enzyme family have been employed in several practical applications: (i) biocatalytic preparation of optically pure building-blocks for organic synthesis; (ii) recycling of by-products from chemical processes; (iii) bioremediation of toxic environmental pollutants; (iv) decontamination of warfare agents; (v) biosensing of environmental pollutants; and (vi) protein tagging for cell imaging and protein analysis. This review discusses the application of HLDs in the context of the biochemical properties of individual enzymes. Further extension of HLD uses within the field of biotechnology will require currently limiting factors - such as low expression, product inhibition, insufficient enzyme selectivity, low affinity and catalytic efficiency towards selected substrates, and instability in the presence of organic co-solvents - to be overcome. We propose that strategies based on protein engineering and isolation of novel HLDs from extremophilic microorganisms may offer solutions.
The X-ray structure of cold-active beta-galactosidase (isoenzyme C-2-2-1) from an Antarctic bacterium Arthrobacter sp. C2-2 was solved at 1.9A resolution. The enzyme forms 660 kDa hexamers with active sites opened to the central cavity of the hexamer and connected by eight channels with exterior solvent. To our best knowledge, this is the first cold-active beta-galactosidase with known structure and also the first known beta-galactosidase structure in the form of compact hexamers. The hexamer organization regulates access of substrates and ligands to six active sites and this unique packing, present also in solution, raises questions about its purpose and function. This enzyme belongs to glycosyl hydrolase family 2, similarly to Escherichia coli beta-galactosidase, forming tetramers necessary for its enzymatic function. However, we discovered significant differences between these two enzymes affecting the ability of tetramer/hexamer formation and complementation of the active site. This structure reveals new insights into the cold-adaptation mechanisms of enzymatic pathways of extremophiles.
- MeSH
- Arthrobacter enzymologie MeSH
- bakteriální proteiny genetika chemie metabolismus MeSH
- beta-galaktosidasa genetika chemie metabolismus MeSH
- financování organizované MeSH
- ionty chemie MeSH
- krystalografie rentgenová MeSH
- kvarterní struktura proteinů MeSH
- lidé MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- nízká teplota MeSH
- rozpouštědla chemie MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
Oxford paperback reference
2nd ed. 597 s. ; 20 cm
2nd ed. VII, 411 s. : il. ; 24 cm
