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Verma J, Sourirajan A, Dev K. Bacterial diversity in 110 thermal hot springs of Indian Himalayan Region (IHR). 3 Biotech 2022; 12:238. [PMID: 36003895 PMCID: PMC9393120 DOI: 10.1007/s13205-022-03270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Thermal hot springs are present throughout the world and constitute a unique habitat for microbial diversity. The current investigation is conducted to study the bacterial diversity of thermophilic microorganisms in thermal hot springs of the Indian Himalayan Region (IHR). As of today, 110 geothermal hot springs have been explored for microbial diversity. In this study, we observed that the growth of thermophilic bacteria isolated from thermal hot springs of IHR ranges between 40 and 100 °C, and pH of 3.5-8 have been reported in the literature. The major bacterial species reported from the thermal hot springs of IHR are Bacillus spp., Geobacillus spp., Paenibacillus spp., Pseudomonas spp., Anoxybacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Thermus aquaticus, Aquimonas, Flavobacterium, etc. Furthermore, bacterial isolates from thermal hot springs of IHR have been reported to produce various enzymes and metabolites such as amylase, β-galactosidase, cellulase, nitrate reductase, acetoin, caffeine degradation enzymes, lipase, urease, and laccase. Metagenomic study and the entire genomic shotgun project have established the impact of physicochemical parameters (temperature and pH) on developing the microbiome. We have discussed the discoveries of microbiological data on the hot springs of IHR until the end of year 2021. As a whole, the microbiome adapts themselves as successful inhabitants to extreme environmental conditions and also serves as a diverse resource for potential applications in health, food, and environment.
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Affiliation(s)
- Jagdish Verma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
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Martin G, Sharma S, Ryan W, Srinivasan NK, Senko JM. Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems. Front Microbiol 2021; 12:675628. [PMID: 34262541 PMCID: PMC8273512 DOI: 10.3389/fmicb.2021.675628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Thermoelectric power generation from coal requires large amounts of water, much of which is used for wet flue gas desulfurization (wFGD) systems that minimize sulfur emissions, and consequently, acid rain. The microbial communities in wFGDs and throughout thermoelectric power plants can influence system performance, waste processing, and the long term stewardship of residual wastes. Any microorganisms that survive in wFGD slurries must tolerate high total dissolved solids concentrations (TDS) and temperatures (50–60°C), but the inocula for wFGDs are typically from fresh surface waters (e.g., lakes or rivers) of low TDS and temperatures, and whose activity might be limited under the physicochemically extreme conditions of the wFGD. To determine the extents of microbiological activities in wFGDs, we examined the microbial activities and communities associated with three wFGDs. O2 consumption rates of three wFGD slurries were optimal at 55°C, and living cells could be detected microscopically, indicating that living and active communities of organisms were present in the wFGD and could metabolize at the high temperature of the wFGD. A 16S rRNA gene-based survey revealed that the wFGD-associated microbial communities included taxa attributable to both thermophilic and mesophilic lineages. Metatranscriptomic analysis of one of the wFGDs indicated an abundance of active Burholderiaceae and several Gammaproteobacteria, and production of transcripts associated with carbohydrate metabolism, osmotic stress response, as well as phage, prophages, and transposable elements. These results illustrate that microbial activities can be sustained in physicochemically extreme wFGDs, and these activities may influence the performance and environmental impacts of thermoelectric power plants.
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Affiliation(s)
- Gregory Martin
- Department of Biology, The University of Akron, Akron, OH, United States
| | - Shagun Sharma
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States
| | - William Ryan
- Department of Biology, The University of Akron, Akron, OH, United States
| | | | - John M Senko
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States.,Department of Geosciences, The University of Akron, Akron, OH, United States
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Prokaryotic and eukaryotic diversity in hydrothermal continental systems. Arch Microbiol 2021; 203:3751-3766. [PMID: 34143270 DOI: 10.1007/s00203-021-02416-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
The term extremophile was suggested more than 30 years ago and represents microorganisms that are capable of developing and living under extreme conditions, these conditions being particularly hostile to other types of microorganisms and to humankind. In terrestrial hydrothermal sites, like hot springs, "mud pools", solfataras, and geysers, the dominant extreme conditions are high temperature, low or high pH, and high levels of salinity. The diversity of microorganisms inhabiting these sites is determined by the conditions of the environment. Organisms belonging to the domains Archaea and Bacteria are more represented than the one belonging to Eukarya. Eukarya members tend to be less present because of their lower tolerance to higher temperatures, however, they perform important ecosystem processes when present. Both prokaryotes and eukaryotes have morphological and physical adaptations that allow them to colonize extreme environments. Microbial mats are complex associations of microorganisms that help the colonization of more extreme systems. In this review, a characterization of prokaryotic and eukaryotic organisms that populate terrestrial hydrothermal systems are made.
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Li J, Pan A, Xie M, Zhang P, Gu X. Characterization of a thermostable κ-carrageenase from a hot spring bacterium and plant protection activity of the oligosaccharide enzymolysis product. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:1812-1819. [PMID: 30255626 DOI: 10.1002/jsfa.9374] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Seaweed oligosaccharides are environmentally-friendly natural products and their use for disease control in sustainable agriculture is extremely promising. Enzymatic digestion to prepare seaweed oligosaccharides has drawn considerable interest. However, the study of enzymatically degraded products of carrageenan is still in its infancy compared with that of other hydrocolloids such as agar and alginate. To prepare degraded carrageenan on a commercial scale, it is necessary to select superior producer bacterial strains to improve the yield and thermostability of carrageenases. RESULTS The carrageenan-degrading bacterium Bacillus sp. HT19 was isolated from sediment of a hot spring in Indonesia, and a κ-carrageenase with high activity was purified from the culture supernatant. The purified enzyme, named Car19, had maximum activity (538 U mg-1 ) at 60 °C and pH 7.0. Notably, the enzyme retained >90% of its initial activity after incubation at 60 °C for 24 h. The Ca2+ obviously improved the thermostability of Car19 at 70 °C. The Km and Vmax values of purified Car19 were 0.061 mg mL-1 and 115.13 U mg-1 , respectively, with κ-carrageenan as substrate. Thin-layer chromatography and electrospray ionization mass-spectrometry analysis of hydrolysates indicated that the enzyme exolytically depolymerized κ-carrageenan to neo-carrabiose. The hydrolysate enhanced the resistance of cucumber to cucumber mosaic virus and increased the activity of antioxidant enzymes in infected plants. CONCLUSION To our knowledge, Car19 is the most thermostable κ-carrageenase reported so far. Its high optimal reaction temperature and thermostability, and unitary hydrolysate constituent, makes Car19 a promising candidate for the preparation of carrageenan oligosaccharides with plant protection activity. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jiang Li
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
| | - Aihong Pan
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P. R. China
| | - Maisheng Xie
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
| | - Pingping Zhang
- College of Biological Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, P. R. China
| | - Xiaoqian Gu
- Key Laboratory of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration, Qingdao, P. R. China
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sibanda T, Selvarajan R, Tekere M. Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms. Microb Biotechnol 2017; 10:570-585. [PMID: 28224723 PMCID: PMC5404200 DOI: 10.1111/1751-7915.12602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/02/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture‐ and molecular‐based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 and Citrobacter sp. PCW7 were able to degrade benzanthracene, naphthalene and diesel oil, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 could produce cellulase enzyme, while Proteus sp. BPS2, Pseudomonas sp. SAS8 and Proteus sp. CAL3 could produce lipase. GC‐MS analysis of bacterial secondary metabolites resulted in identification of 107 different compounds produced by Proteus sp. BPS2, Paenibacillus sp. CAC12, Pseudomonas sp. SAS8, Proteus sp. CAL3 and Paenibacillus sp. CAC13. Most of the compounds identified by both GC‐MS and LC‐MS have previously been determined to have antibacterial, antifungal and/or anticancer properties. Further, microbial metabolites which have previously been known to be produced only by plants or microorganisms found in natural extreme environments were also identified in this study. This research has revealed the immense bioresource potential of microorganisms inhabiting synthetic extreme environments.
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Affiliation(s)
- Timothy Sibanda
- Department of Environmental Sciences, College of Agriculture and Environmental Science, UNISA Florida Campus, PO Box X6, Florida, 1709, South Africa
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agriculture and Environmental Science, UNISA Florida Campus, PO Box X6, Florida, 1709, South Africa
| | - Memory Tekere
- Department of Environmental Sciences, College of Agriculture and Environmental Science, UNISA Florida Campus, PO Box X6, Florida, 1709, South Africa
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Landreau M, Duthoit F, Claeys-Bruno M, Vandenabeele-Trambouze O, Aubry T, Godfroy A, Le Blay G. Entrapment of anaerobic thermophilic and hyperthermophilic marine micro-organisms in a gellan/xanthan matrix. J Appl Microbiol 2016; 120:1531-41. [DOI: 10.1111/jam.13118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/06/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- M. Landreau
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Institut Universitaire Européen de la Mer (IUEM); Université de Bretagne Occidentale; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; IFREMER; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Centre National de la Recherche Scientifique; Technopôle Brest Iroise; Plouzané France
| | - F. Duthoit
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Institut Universitaire Européen de la Mer (IUEM); Université de Bretagne Occidentale; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; IFREMER; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Centre National de la Recherche Scientifique; Technopôle Brest Iroise; Plouzané France
| | | | - O. Vandenabeele-Trambouze
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Institut Universitaire Européen de la Mer (IUEM); Université de Bretagne Occidentale; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; IFREMER; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Centre National de la Recherche Scientifique; Technopôle Brest Iroise; Plouzané France
| | - T. Aubry
- LIMATB; Laboratoire d'Ingénierie des Matériaux de Bretagne/Equipe Rhéologie; U.F.R. Sciences et Techniques; Brest France
| | - A. Godfroy
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Institut Universitaire Européen de la Mer (IUEM); Université de Bretagne Occidentale; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; IFREMER; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Centre National de la Recherche Scientifique; Technopôle Brest Iroise; Plouzané France
| | - G. Le Blay
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Institut Universitaire Européen de la Mer (IUEM); Université de Bretagne Occidentale; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; IFREMER; Technopôle Brest Iroise; Plouzané France
- UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; Centre National de la Recherche Scientifique; Technopôle Brest Iroise; Plouzané France
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Badhai J, Ghosh TS, Das SK. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. Front Microbiol 2015; 6:1166. [PMID: 26579081 PMCID: PMC4620158 DOI: 10.3389/fmicb.2015.01166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.
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Affiliation(s)
- Jhasketan Badhai
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
| | | | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
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Sarmiento F, Peralta R, Blamey JM. Cold and Hot Extremozymes: Industrial Relevance and Current Trends. Front Bioeng Biotechnol 2015; 3:148. [PMID: 26539430 PMCID: PMC4611823 DOI: 10.3389/fbioe.2015.00148] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
The development of enzymes for industrial applications relies heavily on the use of microorganisms. The intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. Extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. These microorganisms have developed unique mechanisms and molecular means to cope with extreme temperatures, acidic and basic pH, high salinity, high radiation, low water activity, and high metal concentrations among other environmental conditions. Extremophile-derived enzymes, or extremozymes, are able to catalyze chemical reactions under harsh conditions, like those found in industrial processes, which were previously not thought to be conducive for enzymatic activity. Due to their optimal activity and stability under extreme conditions, extremozymes offer new catalytic alternatives for current industrial applications. These extremozymes also represent the cornerstone for the development of environmentally friendly, efficient, and sustainable industrial technologies. Many advances in industrial biocatalysis have been achieved in recent years; however, the potential of biocatalysis through the use of extremozymes is far from being fully realized. In this article, the adaptations and significance of psychrophilic, thermophilic, and hyperthermophilic enzymes, and their applications in selected industrial markets will be reviewed. Also, the current challenges in the development and mass production of extremozymes as well as future prospects and trends for their biotechnological application will be discussed.
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Affiliation(s)
| | - Rocío Peralta
- Fundación Científica y Cultural Biociencia , Santiago , Chile
| | - Jenny M Blamey
- Swissaustral USA , Athens, GA , USA ; Fundación Científica y Cultural Biociencia , Santiago , Chile
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Li X, Fu L, Li Z, Ma X, Xiao X, Xu J. Genetic tools for the piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles 2014; 19:59-67. [PMID: 25391810 DOI: 10.1007/s00792-014-0705-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/28/2014] [Indexed: 11/30/2022]
Abstract
The hyperthermophile Pyrococcus yayanosii CH1 is the only high-pressure-requiring microorganism obtained thus far within the archaea domain or among all non-psychrophiles in any domain. In this study, we developed a genetic manipulation system for P. yayanosii after first isolating a facultatively piezophilic derivative strain, designated P. yayanosii A1. The 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase gene was overexpressed in strain P. yayanosii A1 and was demonstrated to confer host cell resistance against simvastatin. Furthermore, using simvastatin as a selection marker, the endogenous pyrF of P. yayanosii A1 was disrupted through homologous recombination, thus generating the additional host strain P. yayanosii A2 (ΔpyrF). A markerless gene disruption vector was constructed by incorporating a pyrF-sim (R) cassette that enables the combined use of simvastatin resistance for positive selection and 5-FOA for counter selection. The utility of this versatile disruption system was demonstrated by deleting the carbon-nitrogen hydrolase of P. yayanosii strain A1. These results demonstrate that a variety of genetic tools are now in place to study unknown gene function and the molecular mechanisms of piezophilic adaptation in P. yayanosii.
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Affiliation(s)
- Xuegong Li
- Institute of Oceanology, Shanghai Jiao Tong University, Minhang Dongchuan Road 800, Shanghai, 200240, China
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Bacterial extremo-α-carbonic anhydrases from deep-sea hydrothermal vents as potential biocatalysts for CO2 sequestration. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Purification and characterization of a thermostable λ-carrageenase from a hot spring bacterium, Bacillus sp. Biotechnol Lett 2014; 36:1669-74. [DOI: 10.1007/s10529-014-1520-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/20/2014] [Indexed: 01/24/2023]
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Reich S, Kress N, Nestl BM, Hauer B. Variations in the stability of NCR ene reductase by rational enzyme loop modulation. J Struct Biol 2014; 185:228-33. [DOI: 10.1016/j.jsb.2013.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/15/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
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Toesch M, Schober M, Faber K. Microbial alkyl- and aryl-sulfatases: mechanism, occurrence, screening and stereoselectivities. Appl Microbiol Biotechnol 2014; 98:1485-96. [PMID: 24352732 PMCID: PMC3920027 DOI: 10.1007/s00253-013-5438-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 01/18/2023]
Abstract
This review gives an overview on the occurrence of sulfatases in Prokaryota, Eukaryota and Archaea. The mechanism of enzymes acting with retention or inversion of configuration during sulfate ester hydrolysis is discussed taking two complementary examples. Methods for the discovery of novel alkyl sulfatases are described by way of sequence-based search and enzyme induction. A comprehensive list of organisms with their respective substrate scope regarding prim- and sec-alkyl sulfate esters allows to assess the capabilities and limitations of various biocatalysts employed as whole cell systems or as purified enzymes with respect to their activities and enantioselectivities. Methods for immobilization and selectivity enhancement by addition of metal ions or organic (co)solvents are summarised.
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Affiliation(s)
- Michael Toesch
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Markus Schober
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Kurt Faber
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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15
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Eram MS, Ma K. Decarboxylation of pyruvate to acetaldehyde for ethanol production by hyperthermophiles. Biomolecules 2013; 3:578-96. [PMID: 24970182 PMCID: PMC4030962 DOI: 10.3390/biom3030578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/02/2013] [Accepted: 08/15/2013] [Indexed: 11/16/2022] Open
Abstract
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. The only PDC activity reported in hyperthermophiles was a bifunctional, TPP- and CoA-dependent pyruvate ferredoxin oxidoreductase (POR)/PDC enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. Another enzyme known to be involved in catalysis of acetaldehyde production from pyruvate is CoA-acetylating acetaldehyde dehydrogenase (AcDH encoded by mhpF and adhE). Pyruvate is oxidized into acetyl-CoA by either POR or pyruvate formate lyase (PFL), and AcDH catalyzes the reduction of acetyl-CoA to acetaldehyde in mesophilic organisms. AcDH is present in some mesophilic (such as clostridia) and thermophilic bacteria (e.g., Geobacillus and Thermoanaerobacter). However, no AcDH gene or protein homologs could be found in the released genomes and proteomes of hyperthermophiles. Moreover, no such activity was detectable from the cell-free extracts of different hyperthermophiles under different assay conditions. In conclusion, no commonly-known PDCs was found in hyperthermophiles. Instead of the commonly-known PDC, it appears that at least one multifunctional enzyme is responsible for catalyzing the non-oxidative decarboxylation of pyruvate to acetaldehyde in hyperthermophiles.
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
| | - Kesen Ma
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
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Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:859264. [PMID: 22844640 PMCID: PMC3403428 DOI: 10.1155/2012/859264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 12/03/2022]
Abstract
Species belonging to the order Aquificales are believed to be an early branching lineage within the Bacteria. However, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the Aquificales should be grouped with ε-proteobacteria. To investigate the phylogenetic position of Aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six Aquificales species based on the concatenated data of proteins shared by these bacteria. In the phylogenetic tree based on the whole-genome information, Aquificales was more closely related to Thermotogales than to Proteobacteria, suggesting that the Aquificales is a relatively early branching lineage within the Bacteria. Moreover, we classified the phylogenetic tree of each conserved orthologous protein by its topology. As a result, in the most major type of the phylogenetic trees, Aquificales was closely related to the Thermotogales. However, Aquificales was closely related to ε-proteobacteria in 21.0% of all phylogenetic trees, suggesting that many proteins phylogenetically related to the ε-proteobacteria may be encoded in the genomes of the members of the Aquificales. This unique feature may be responsible for the high variability in the branching order of Aquificales in single-gene phylogenetic trees.
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Shyam Prasad G, Girisham S, Reddy SM. Potential of Thermophilic Fungus Rhizomucor pusillus NRRL 28626 in Biotransformation of Antihelmintic Drug Albendazole. Appl Biochem Biotechnol 2011; 165:1120-8. [DOI: 10.1007/s12010-011-9329-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 07/27/2011] [Indexed: 10/17/2022]
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Kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic Archaea at extremely low pH of 1.1-1.3. Appl Microbiol Biotechnol 2011; 93:1295-303. [PMID: 21751006 PMCID: PMC3264884 DOI: 10.1007/s00253-011-3460-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 06/20/2011] [Accepted: 06/20/2011] [Indexed: 11/18/2022]
Abstract
The extreme acid conditions required for scorodite (FeAsO4·2H2O) biomineralization (pH below 1.3) are suboptimal for growth of most thermoacidophilic Archaea. With the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic Archaea at low pH conditions. Ferrous iron oxidation rates were determined in batch-cultures at pH 1.3 and a temperature of 75°C for Acidianus sulfidivorans, Metallosphaera prunea and a mixed Sulfolobus culture. Ferrous iron and CO2 in air were added as sole energy and carbon source. The highest growth rate (0.066 h−1) was found with the mixed Sulfolobus culture. Therefore, this culture was selected for further experiments. Growth was not stimulated by increase of the CO2 concentration or by addition of sulphur as an additional energy source. In a CSTR operated at the suboptimal pH of 1.1, the maximum specific growth rate of the mixed culture was 0.022 h−1, with ferrous iron oxidation rates of 1.5 g L−1 d−1. Compared to pH 1.3, growth rates were strongly reduced but the ferrous iron oxidation rate remained unaffected. Influent ferrous iron concentrations above 6 g L−1 caused instability of Fe2+ oxidation, probably due to product (Fe3+) inhibition. Ferric-containing, nano-sized precipitates of K-jarosite were found on the cell surface. Continuous cultivation stimulated the formation of an exopolysaccharide-like substance. This indicates that biofilm formation may provide a means of biomass retention. Our findings showed that stable continuous cultivation of a mixed iron-oxidizing culture is feasible at the extreme conditions required for continuous biomineral formation.
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Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond. Naturwissenschaften 2011; 98:253-79. [DOI: 10.1007/s00114-011-0775-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 01/27/2023]
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Sharma D, Sharma B, Shukla A. Biotechnological Approach of Microbial Lipase: A Review. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/biotech.2011.23.40] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Identification of various substrate-binding proteins of the hyperthermophylic archaeon Aeropyrum pernix K1. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Adalbjörnsson BV, Toogood HS, Fryszkowska A, Pudney CR, Jowitt TA, Leys D, Scrutton NS. Biocatalysis with Thermostable Enzymes: Structure and Properties of a Thermophilic ‘ene’-Reductase related to Old Yellow Enzyme. Chembiochem 2009; 11:197-207. [DOI: 10.1002/cbic.200900570] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Khosravi-Darani K, Vasheghani-Farahani E. Application of Supercritical Fluid Extraction in Biotechnology. Crit Rev Biotechnol 2008; 25:231-42. [PMID: 16419619 DOI: 10.1080/07388550500354841] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the present paper recent investigations on the applications of supercritical fluid extraction (SCE) from post fermentation biomass or in situ extraction of inhibitory fermentation products as a promising method for increasing the yield of extraction have been reviewed. Although supercritical CO2 (SC-CO2) is unfriendly, or even toxic, for some living cells and precludes direct fermentation in dense CO2, it does not rule out other useful applications for in situ extraction of inhibitory fermentation products and fractional extraction of biomass constituents. This technique is a highly desirable method for fractional extraction of biomass constituents, and intracellular metabolites due to the potential of system modification by physical parameters and addition of co-solvents to selectively extract compounds of different polarity, volatility and hydrophilicity without any contamination.
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Affiliation(s)
- K Khosravi-Darani
- Department of Chemical Engineering, Tarbiat Modarres University, Tehran, IR Iran
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Bannikova GE, Lopatin SA, Varlamov VP, Kuznetsov BB, Kozina IV, Miroshnichenko ML, Chernykh NA, Turova TP, Bonch-Osmolovskaya EA. The thermophilic bacteria hydrolyzing agar: Characterization of thermostable agarase. APPL BIOCHEM MICRO+ 2008. [DOI: 10.1134/s0003683808040054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Alteration of metal ions improves the activity and thermostability of aminoacylase from hyperthermophilic archaeon Pyrococcus horikoshii. Biotechnol Lett 2008; 30:1639-43. [DOI: 10.1007/s10529-008-9737-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 03/26/2008] [Accepted: 03/31/2008] [Indexed: 10/22/2022]
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Abstract
Enzymes that are naturally found in thermophilic and hyperthermophilic organisms are being used as robust biocatalysts in the fine chemical and pharmaceutical industries. They have important use in these industries due to their increased stability which is often required during commercial reaction conditions. The approach used in these studies is to learn how nature has managed to stabilize these proteins using a detailed knowledge of their biochemical properties and three-dimensional structures. This is illustrated with several different classes of enzyme that have been studied at Exeter. These include alcohol dehydrogenase, aminoacylase, pyroglutamyl carboxypeptidase, gamma-lactamase, dehalogenase and lysophospholipase.
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Tanimoto K, Higashi N, Nishioka M, Ishikawa K, Taya M. Characterization of thermostable aminoacylase from hyperthermophilic archaeon Pyrococcus horikoshii. FEBS J 2008; 275:1140-9. [DOI: 10.1111/j.1742-4658.2008.06274.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gadler P, Faber K. Highly Enantioselective Biohydrolysis ofsec-Alkyl Sulfate Esters with Inversion of Configuration Catalysed byPseudomonas spp. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700637] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology.
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Affiliation(s)
- Elena V Pikuta
- National Space Sciences and Technology Center, NASA, Astrobiology Laboratory, Huntsville, Alabama 35805, USA.
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Ehrhardt CJ, Haymon RM, Lamontagne MG, Holden PA. Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise. Environ Microbiol 2007; 9:900-12. [PMID: 17359262 DOI: 10.1111/j.1462-2920.2006.01211.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Little is known about the fluids or the microbial communities present within potentially vast hydrothermal reservoirs contained in still-hot volcanic ocean crust beneath the flanks of the mid-ocean ridge. During Alvin dives in 2002, organic material attached to basalt was collected at low, near-ambient temperatures from an abyssal hill fault scarp in 0.5 Ma lithosphere on the western ridge flank of the East Pacific Rise. Mineral analysis by X-ray diffractometry and scanning electron microscopy revealed high-temperature (> 110 degrees C) phases chalcopyrite (Cu(5)FeS(4)) and 1C pyrrhotite (Fe(1-x)S) within the fault scarp materials. A molecular survey of archaeal genes encoding 16S rRNA identified a diverse hyperthermophilic community, including groups within Crenarchaeota, Euryarchaeota, and Korarchaeota. We propose that the sulfide, metals and archaeal communities originated within a basalt-hosted subseafloor hydrothermal habitat beneath the East Pacific Rise ridge flank and were transported to the seafloor during a recent episode of hydrothermal venting from the abyssal hill fault. Additionally, inferred metabolisms from the fault scarp community suggest that an ecologically unique high-temperature archaeal biosphere may thrive beneath the young East Pacific Rise ridge flank and that abyssal hill fault scarps may present new opportunities for sampling for this largely unexplored microbial habitat.
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Synowiecki J, Grzybowska B, Zdziebło A. Sources, Properties and Suitability of New Thermostable Enzymes in Food Processing. Crit Rev Food Sci Nutr 2007; 46:197-205. [PMID: 16527752 DOI: 10.1080/10408690590957296] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Investigations concerning recombinant a-amylases from Pyrococcus woesei and thermostable a-glucosidase from Thermus thermophilus indicate their suitability for starch processing. Furthermore, the study of recombinant ss-galactosidase from Pyrococcus woesei suitable for purpose of low lactose milk and whey production are also presented. The activity of this enzyme in a wide pH range of 4.3-6.6 and high thermostability suggests that it can be used for processing of dairy products at temperatures which restrict microbial growth during a long operating time of continuous-flow reactor with an immobilized enzyme system. Preparation of recombinant a-amylase and ss-galactosidase was facilitated by cloning and expression of genes from Pyrococcus woesei in Escherichia coli host. Satisfactory level of recombinant enzymes purification was achieved by thermal precipitation of native proteins originated from Escherichia coli. The obtained a-amylase has maximal activity at pH 5.6 and 93 degrees C. The half-life of this preparation (pH 5.6) at 90 degrees C and 110 degrees C was 11 h and 3.5 h, respectively, and retained 24% of residual activity following incubation for 2 h at 120 degrees C. An advantageous attribute of recombinant a -amylase is independence of its activity and stability on calcium salt. a-Glucosidase from Thermus thermophilus also not require metal ions for stability and retained about 80% of maximal activity at pH range 5.8-6.9. Thus, this enzyme can be used together with recombinant a-amylase.
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Affiliation(s)
- Józef Synowiecki
- Department of Food Chemistry, Technology and Biotechnology, Chemical Faculty, Gdansk University of Technology, ul. Gabriela Narutowicza 11/12, 80-952, Gdansk, Poland.
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Kaksonen AH, Plumb JJ, Robertson WJ, Spring S, Schumann P, Franzmann PD, Puhakka JA. Novel thermophilic sulfate-reducing bacteria from a geothermally active underground mine in Japan. Appl Environ Microbiol 2006; 72:3759-62. [PMID: 16672530 PMCID: PMC1472396 DOI: 10.1128/aem.72.5.3759-3762.2006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermophilic sulfate-reducing bacteria were enriched from samples obtained from a geothermal underground mine in Japan. The enrichment cultures contained bacteria affiliated with the genera Desulfotomaculum, Thermanaeromonas, Thermincola, Thermovenabulum, Moorella, "Natronoanaerobium," and Clostridium. Two novel thermophilic sulfate-reducing strains, RL50JIII and RL80JIV, affiliated with the genera Desulfotomaculum and Thermanaeromonas, respectively, were isolated.
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Affiliation(s)
- Anna H Kaksonen
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland.
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Kranner I, Birtić S, Anderson KM, Pritchard HW. Glutathione half-cell reduction potential: a universal stress marker and modulator of programmed cell death? Free Radic Biol Med 2006; 40:2155-65. [PMID: 16785029 DOI: 10.1016/j.freeradbiomed.2006.02.013] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 02/16/2006] [Accepted: 02/17/2006] [Indexed: 01/18/2023]
Abstract
The elucidation of factors that contribute to cell viability loss is presently compromised by the lack of a universal measure that quantifies "stress." We have investigated mechanisms of viability loss in plant seeds to find a reliable marker of stress response. Oxidative damage has previously been correlated with degenerative processes and death, but how exactly this contributes to viability loss is unknown. We show in four species subjected to ageing or desiccation that seed viability decreased by 50% when the half-cell reduction potential of glutathione (E(GSSG/2GSH)), a major cellular antioxidant and redox buffer, increased to -180 to -160 mV. We then conducted a metaanalysis of data representative of 13 plant and fungal orders to show that plant stress generally becomes lethal when E(GSSG/2GSH) exceeds -160 mV. We put forward that this change in E(GSSG/2GSH) is part of the signaling cascade that initiates programmed cell death (PCD), finally causing internucleosomal DNA fragmentation in the final, or execution phase, of PCD. E(GSSG/2GSH) is therefore a universal marker of plant cell viability and allows us to predict whether a seed will live, germinate, and produce a new plant, or if it will die.
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Affiliation(s)
- Ilse Kranner
- Seed Conservation Department, Royal Botanic Gardens, Kew, Wakehurst Place, West Sussex RH17 6TN, UK.
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Gödde C, Sahm K, Brouns SJJ, Kluskens LD, van der Oost J, de Vos WM, Antranikian G. Cloning and expression of islandisin, a new thermostable subtilisin from Fervidobacterium islandicum, in Escherichia coli. Appl Environ Microbiol 2005; 71:3951-8. [PMID: 16000809 PMCID: PMC1168981 DOI: 10.1128/aem.71.7.3951-3958.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene encoding a subtilisin-like protease, designated islandisin, from the extremely thermophilic bacterium Fervidobacterium islandicum (DSMZ 5733) was cloned and actively expressed in Escherichia coli. The gene was identified by PCR using degenerated primers based on conserved regions around two of the three catalytic residues (Asp, His, and Ser) of subtilisin-like serine protease-encoding genes. Using inverse PCR regions flanking the catalytic residues, the gene could be cloned. Sequencing revealed an open reading frame of 2,106 bp. The deduced amino acid sequence indicated that the enzyme is synthesized as a proenzyme with a putative signal sequence of 33 amino acids (aa) in length. The mature protein contains the three catalytic residues (Asp177, His215, and Ser391) and has a length of 668 aa. Amino acid sequence comparison and phylogenetic analysis indicated that this enzyme could be classified as a subtilisin-like serine protease in the subgroup of thermitase. The whole gene was amplified by PCR, ligated into pET-15b, and successfully expressed in E. coli BL21(DE3)pLysS. The recombinant islandisin was purified by heat denaturation, followed by hydroxyapatite chromatography. The enzyme is active at a broad range of temperatures (60 to 80 degrees C) and pHs (pH 6 to 8.5) and shows optimal proteolytic activity at 80 degrees C and pH 8.0. Islandisin is resistant to a number of detergents and solvents and shows high thermostability over a long period of time (up to 32 h) at 80 degrees C with a half-life of 4 h at 90 degrees C and 1.5 h at 100 degrees C.
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Affiliation(s)
- Carolin Gödde
- Institute of Technical Microbiology, Technical University Hamburg-Harburg, Kasernenstr. 12, D-21073 Hamburg, Germany
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Martin PD, Purcarea C, Zhang P, Vaishnav A, Sadecki S, Guy-Evans HI, Evans DR, Edwards BFP. The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex aeolicus at 1.7Å Resolution. J Mol Biol 2005; 348:535-47. [PMID: 15826652 DOI: 10.1016/j.jmb.2005.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 02/28/2005] [Accepted: 03/03/2005] [Indexed: 11/16/2022]
Abstract
Dihydroorotases (EC 3.5.2.3) catalyze the reversible cyclization of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The X-ray structures of Aquifex aeolicus dihydroorotase in two space groups, C222(1) and C2, were determined at a resolution of 1.7A. These are the first structures of a type I dihydroorotase, a class of molecules that includes the dihydroorotase domain of mammalian CAD. The type I enzymes are more ancient and larger, at 45 kDa, than the type II enzymes exemplified by the 38 kDa Escherichia coli dihydroorotase. Both dihydroorotases are members of the metallo-dependent hydrolase superfamily, whose members have a distorted "TIM barrel" domain containing the active site. However, A.aeolicus dihydroorotase has a second, composite domain, which the E.coli enzyme lacks and has only one of the two zinc atoms present in the E.coli enzyme. A.aeolicus dihydroorotase is unique in exhibiting significant activity only when complexed with aspartate transcarbamoylase, whereas the E.coli dihydroorotase and the CAD dihydroorotase domain are active as free proteins. The latency of A.aeolicus dihydroorotase can be related to two differences between its structure and that of E.coli dihydroorotase: (1) the monoclinic structure has a novel cysteine ligand to the zinc that blocks the active site and possibly functions as a "cysteine switch"; and (2) active site residues that bind the substrate in E.coli dihydroorotase are located in disordered loops in both crystal structures of A.aeolicus dihydroorotase and may function as a disorder-to-order "entropy switch".
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Affiliation(s)
- Philip D Martin
- Wayne State University School of Medicine, Department of Biochemistry and Molecular Biology, 540 E. Canfield, Detroit, MI 48201, USA
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Hirayama H, Takai K, Inagaki F, Yamato Y, Suzuki M, Nealson KH, Horikoshi K. Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine. Extremophiles 2005; 9:169-84. [PMID: 15776216 DOI: 10.1007/s00792-005-0433-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 12/28/2004] [Indexed: 11/29/2022]
Abstract
Change of bacterial community occurring along a hot water stream in the Hishikari gold mine, Japan, was investigated by applying a combination of various culture-independent techniques. The stream, which is derived from a subsurface anaerobic aquifer containing plentiful CO2, CH4, H2, and NH4+, emerges in a mine tunnel 320 m below the surface providing nutrients for a lush microbial community that extends to a distance of approximately 7 m in the absence of sunlight-irradiation. Over this distance, the temperature decreases from 69 degrees C to 55 degrees C, and the oxidation-reduction potential increases from -130 mV to +59 mV. In the hot upper reaches of the stream, the dominant phylotypes were: 1) a deeply branching lineage of thermophilic methane-oxidizing gamma-Proteobacteria, and 2) a thermophilic hydrogen- and sulfur-oxidizing Sulfurihydrogenibium sp. In contrast, the prevailing phylotypes in the middle and lower parts of the stream were closely related to ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira spp.. Changes in the microbial metabolic potential estimated by competitive PCR analysis of genes encoding the enzymes, particulate methane monooxygenase (pmoA), ammonia monooxygenase (amoA), and putative nitrite oxidoreductase (norB), also substantiated the community shift indicated by 16S rRNA gene analysis. The diversity of putative norB lineages was assessed for the first time in the hot water environment. Estimation of dominant phylotypes by whole-cell fluorescent in situ hybridization and changes in inorganic nitrogen compounds such as decreasing ammonium and increasing nitrite and nitrate in the mat-interstitial water along the stream were consistent with the observed transition of the bacterial community structure in the stream.
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Affiliation(s)
- Hisako Hirayama
- Subground Animalcule Retrieval (SUGAR) Project, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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Chapter 10 Non-affinity sensing technology: the exploitation of biocatalytic events for environmental analysis. BIOSENSORS AND MODERN BIOSPECIFIC ANALYTICAL TECHNIQUES 2005. [DOI: 10.1016/s0166-526x(05)44010-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wallner SR, Nestl BM, Faber K. Highly enantioselective stereo-inverting sec-alkylsulfatase activity of hyperthermophilic Archaea. Org Biomol Chem 2005; 3:2652-6. [PMID: 15999201 DOI: 10.1039/b504883d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
rac-sec-Alkyl sulfate esters 1a-8a were resolved in low to excellent enantioselectivities with E-values up to >200 using whole cells of aerobically-grown hyperthermophilic sulfur-metabolizers, such as Sulfolobus solfataricus DSM 1617, Sulfolobus shibatae DSM 5389 and, most notably, Sulfolobus acidocaldarius DSM 639. Significantly enhanced selectivities were obtained using cells grown on sucrose-enriched Brock-medium. The stereochemical course of this biohydrolysis was shown to proceed with strict inversion of configuration, thus the preferred (R)-enantiomers were converted into the corresponding (S)-sec-alcohols to furnish a homochiral product mixture.
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Affiliation(s)
- Sabine R Wallner
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Kinnunen PHM, Puhakka JA. Characterization of iron- and sulphide mineral-oxidizing moderately thermophilic acidophilic bacteria from an Indonesian auto-heating copper mine waste heap and a deep South African gold mine. J Ind Microbiol Biotechnol 2004; 31:409-14. [PMID: 15309637 DOI: 10.1007/s10295-004-0160-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 07/13/2004] [Indexed: 10/26/2022]
Abstract
Iron- and chalcopyrite-oxidizing enrichment cultures were obtained at 50 degrees C from acidic, high-temperature, copper/gold mine environments in Indonesia and South Africa. Over 90% copper yield was obtained from chalcopyrite concentrate with the Indonesian enrichment in 3 months with 2% solids concentration, when pH was maintained at around 2. Neither addition of silver cations nor an enhanced nutrient concentration influenced chalcopyrite leaching. Excision and sequencing of bands from denaturing gradient gel electrophoresis of the amplified partial 16S rRNA gene showed that the enrichment cultures from different environments in South Africa and Indonesia were very simple, and similar. Chalcopyrite concentrate supported a simpler and different community than Fe2+. The members of the enrichment cultures were closely related to Sulfobacillus yellowstonensis and Sulfobacillus acidophilus.
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Affiliation(s)
- Päivi H-M Kinnunen
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, PO Box 541, 33101 Tampere, Finland.
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Abstract
There are currently 35 available nonredundant molecular structures of class-13 alpha-amylases (EC 3.2.1.1), mostly from microbial organisms living under a wide range of environmental conditions. One of the most recent additions has been the first alpha-amylase structure of a hyperthermophilic archaeon [Linden et al., J. Biol. Chem. 2003, 278, 9875-9884]. The structure has been used for comparative analyses with a representative set of three alpha-amylases from thermophilic, mesophilic and psychrophilic sources to identify molecular parameters for environmental adaptation. Our analysis supports generally observed trends such as an increase in structural compactness as well as an increase in salt bridges in order to cope with high-temperature conditions. The two representative thermophilic structures used in this comparative study have independently evolved di-metal centres--not present in the mesophilic and psychrophilic structures--in the vicinity of the active site. These observations may provide impetus for the design of alpha-amylases with improved molecular properties to enhance their utility in biotechnological processes.
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Affiliation(s)
- Anni Linden
- EMBL-Hamburg c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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44
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Toogood HS, Brown RC, Line K, Keene PA, Taylor SJ, McCague R, Littlechild JA. The use of a thermostable signature amidase in the resolution of the bicyclic synthon (rac)-γ-lactam. Tetrahedron 2004. [DOI: 10.1016/j.tet.2003.11.064] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Guy JE, Isupov MN, Littlechild JA. The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix. J Mol Biol 2003; 331:1041-51. [PMID: 12927540 DOI: 10.1016/s0022-2836(03)00857-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structure of the recombinant medium chain alcohol dehydrogenase (ADH) from the hyperthermophilic archaeon Aeropyrum pernix has been solved by the multiple anomalous dispersion technique using the signal from the naturally occurring zinc ions. The enzyme is a tetramer with 222 point group symmetry. The ADH monomer is formed from a catalytic and a cofactor-binding domain, with the overall fold similar to previously solved ADH structures. The 1.62 A resolution A.pernix ADH structure is that of the holo form, with the cofactor NADH bound into the cleft between the two domains. The electron density found in the active site has been interpreted to be octanoic acid, which has been shown to be an inhibitor of the enzyme. This inhibitor is positioned with its carbonyl oxygen atom forming the fourth ligand of the catalytic zinc ion. The structural zinc ion of each monomer is present at only partial occupancy and in its absence a disulfide bond is formed. The enhanced thermal stability of the A.pernix ADH is thought to arise primarily from increased ionic and hydrophobic interactions on the subunit interfaces.
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Affiliation(s)
- Jodie E Guy
- Schools of Chemistry and Biological Sciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
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46
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Marion GM, Fritsen CH, Eicken H, Payne MC. The search for life on Europa: limiting environmental factors, potential habitats, and Earth analogues. ASTROBIOLOGY 2003; 3:785-811. [PMID: 14987483 DOI: 10.1089/153110703322736105] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The putative ocean of Europa has focused considerable attention on the potential habitats for life on Europa. By generally clement Earth standards, these Europan habitats are likely to be extreme environments. The objectives of this paper were to examine: (1) the limits for biological activity on Earth with respect to temperature, salinity, acidity, desiccation, radiation, pressure, and time; (2) potential habitats for life on Europa; and (3) Earth analogues and their limitations for Europa. Based on empirical evidence, the limits for biological activity on Earth are: (1) the temperature range is from 253 to 394 K; (2) the salinity range is a(H2O) = 0.6-1.0; (3) the desiccation range is from 60% to 100% relative humidity; (4) the acidity range is from pH 0 to 13; (5) microbes such as Deinococcus are roughly 4,000 times more resistant to ionizing radiation than humans; (6) the range for hydrostatic pressure is from 0 to 1,100 bars; and (7) the maximum time for organisms to survive in the dormant state may be as long as 250 million years. The potential habitats for life on Europa are the ice layer, the brine ocean, and the seafloor environment. The dual stresses of lethal radiation and low temperatures on or near the icy surface of Europa preclude the possibility of biological activity anywhere near the surface. Only at the base of the ice layer could one expect to find the suitable temperatures and liquid water that are necessary for life. An ice layer turnover time of 10 million years is probably rapid enough for preserving in the surface ice layers dormant life forms originating from the ocean. Model simulations demonstrate that hypothetical oceans could exist on Europa that are too cold for biological activity (T < 253 K). These simulations also demonstrate that salinities are high, which would restrict life to extreme halophiles. An acidic ocean (if present) could also potentially limit life. Pressure, per se, is unlikely to directly limit life on Europa. But indirectly, pressure plays an important role in controlling the chemical environments for life. Deep ocean basins such as the Mariana Trench are good analogues for the cold, high-pressure ocean of Europa. Many of the best terrestrial analogues for potential Europan habitats are in the Arctic and Antarctica. The six factors likely to be most important in defining the environments for life on Europa and the focus for future work are liquid water, energy, nutrients, low temperatures, salinity, and high pressures.
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Hallberg KB, Johnson DB. Biodiversity of acidophilic prokaryotes. ADVANCES IN APPLIED MICROBIOLOGY 2002; 49:37-84. [PMID: 11757351 DOI: 10.1016/s0065-2164(01)49009-5] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- K B Hallberg
- School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, United Kingdom
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48
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Abstract
Extremophlic microorganisms have developed a variety of molecular strategies in order to survive in harsh conditions. For the utilization of natural polymeric substrates such as starch, a number of extremophiles, belonging to different taxonomic groups, produce amylolytic enzymes. This class of enzyme is important not only for the study of biocatalysis and protein stability at extreme conditions but also for the many biotechnological opportunities they offer. In this review, we report on the different molecular properties of thermostable archaeal and bacterial enzymes including alpha-amylase, alpha-glucosidase, glucoamylase, pullulanase, and cyclodextrin glycosyltransferase. Comparison of the primary sequence of the pyrococcal pullulanase with other members of the glucosyl hydrolase family revealed that significant differences are responsible for the mode of action of these enzymes.
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Affiliation(s)
- Costanzo Bertoldo
- Technical University Hamburg-Harburg, Institute of Technical Microbiology, Kasernenstrasse 12, 21073, Hamburg, Germany
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49
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Park CB, Clark DS. Rupture of the cell envelope by decompression of the deep-sea methanogen Methanococcus jannaschii. Appl Environ Microbiol 2002; 68:1458-63. [PMID: 11872502 PMCID: PMC123755 DOI: 10.1128/aem.68.3.1458-1463.2002] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of decompression on the structure of Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen, was studied in a novel high-pressure, high-temperature bioreactor. The cell envelope of M. jannaschii appeared to rupture upon rapid decompression (ca. 1 s) from 260 atm of hyperbaric pressure. When decompression from 260 atm was performed over 5 min, the proportion of ruptured cells decreased significantly. In contrast to the effect produced by decompression from hyperbaric pressure, decompression from a hydrostatic pressure of 260 atm did not induce cell lysis.
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Affiliation(s)
- Chan Beum Park
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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Parker KN, Chhabra SR, Lam D, Callen W, Duffaud GD, Snead MA, Short JM, Mathur EJ, Kelly RM. Galactomannanases Man2 and Man5 from Thermotoga species: growth physiology on galactomannans, gene sequence analysis, and biochemical properties of recombinant enzymes. Biotechnol Bioeng 2001; 75:322-33. [PMID: 11590605 DOI: 10.1002/bit.10020] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The enzymatic hydrolysis of mannan-based hemicelluloses is technologically important for applications ranging from pulp and paper processing to food processing to gas and oil well stimulation. In many cases, thermostability and activity at elevated temperatures can be advantageous. To this end, the genes encoding beta-mannosidase (man2) and beta-mannanase (man5) from the hyperthermophilic bacteria Thermotoga neapolitana 5068 and Thermotoga maritima were isolated, cloned, and expressed in Escherichia coli. The amino acid sequences for the mannosidases from these organisms were 77% identical and corresponded to proteins with an M(r) of approximately 92 kDa. The translated nucleotide sequences for the beta-mannanase genes (man5) encoded polypeptides with an M(r) of 76 kDa that exhibited 84% amino acid sequence identity. The recombinant versions of Man2 and Man5 had similar respective biochemical and biophysical properties, which were also comparable to those determined for the native versions of these enzymes in T. neapolitana. The optimal temperature and pH for the recombinant Man2 and Man5 from both organisms were approximately 90 degrees C and 7.0, respectively. The presence of Man2 and Man5 in these two Thermotoga species indicates that galactomannan is a potential growth substrate. This was supported by the fact that beta-mannanase and beta-mannosidase activities were significantly stimulated when T. neapolitana was grown on guar or carob galactomannan. Maximum cell densities increased by at least tenfold when either guar or carob galactomannan was added to the growth medium. For T. neapolitana grown on guar at 83 degrees C, Man5 was secreted into the culture media, whereas Man2 was intracellular. These localizations were consistent with the presence and lack of signal peptides for Man5 and Man2, respectively. The identification of the galactomannan-degrading enzymes in these Thermotoga species adds to the list of biotechnologically important hemicellulases produced by members of this hyperthermophilic genera.
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Affiliation(s)
- K N Parker
- Department of Chemical Engineering, North Carolina State University, Box 7905, Raleigh, North Carolina 27695-7905, USA
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