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Jose Berenguer - One of the best experts on this subject based on the ideXlab platform.
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Partial and complete denitrification in Thermus thermophilus: Lessons from genome drafts. Biochem Soc Trans 2011, 39:249-253. doi:10.1186/1471-2164-12-577 Cite this article as: Gounder et al.: Sequence of the hyperplastic genome of the naturally competent
2020Co-Authors: Carlos Bricio, Laura Alvarez, Manuel J Gómez, Jose BerenguerAbstract:Abstract We have obtained draft genomic sequences of PD (partial denitrificant) and CD (complete denitrificant) strains of Thermus thermophilus. Their genomes are similar in size to that of the aerobic strains sequenced to date and probably contain a similar megaplasmid. In the CD strain, the genes encoding a putative cytochrome cd 1 Nir (nitrite reductase) and ancillary proteins were clustered with a cytochrome c-dependent Nor (nitric oxide reductase), and with genes that are probably implicated in their regulation. The Nar (nitrate reductase) and associated genes were also clustered and located 7 kb downstream of the genes coding for the Nir. The whole nar-nir-nor denitrification supercluster was identified as part of a variable region of a megaplasmid. No homologues of NosZ were found despite nitrogen balance supports the idea that such activity actually exists. The genus Thermus The genus Thermus is widespread in natural and man-made thermophilic environments all over the world. It includes hundreds of strains that constitute an important source of enzymes of biotechnological interest Among the great panoply of Thermus spp. isolates in existence, T. thermophilus strains HB27 and HB8 have been by far the most studied under laboratory conditions. Bot
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into the Thermus mobilome presence diversity and recent activities of insertion sequences across Thermus spp
Microorganisms, 2019Co-Authors: Alba Blesa, M Sanchez, Eva Sacristanhorcajada, Sandra De La Fuente, Ramon Peiro, Jose BerenguerAbstract:A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
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Hierarchical Control of Nitrite Respiration by Transcription Factors Encoded within Mobile Gene Clusters of Thermus thermophilus
Genes, 2017Co-Authors: Laura Alvarez, Nieves G. Quintáns, Alba Blesa, Ignacio Baquedano, Mario Mencía, Carlos Bricio, Jose BerenguerAbstract:Denitrification in Thermus thermophilus is encoded by the nitrate respiration conjugative element (NCE) and nitrite and nitric oxide respiration (nic) gene clusters. A tight coordination of each cl ...
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role of archaeal hera protein in the biology of the bacterium Thermus thermophilus
Genes, 2017Co-Authors: Alba Blesa, Nieves G. Quintáns, Ignacio Baquedano, Carlos P Mata, Jose R Caston, Jose BerenguerAbstract:Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 A and a bottom module of 95 A. A central pore was detected in the structure that ranges from 13 A at one extreme, to 30 A at the other. Mutants lacking HepA show defective natural competence and DNA donation capability in a conjugation-like process termed “transjugation”, and also high sensitivity to UV and dramatic sensitivity to high temperatures. These data support that acquisition of an ancestral archaeal HerA has been fundamental for the adaptation of Thermus spp. to high temperatures.
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Thermus thermophilus as biological model
Extremophiles, 2009Co-Authors: Felipe Cava, Aurelio Hidalgo, Jose BerenguerAbstract:Thermus spp is one of the most wide spread genuses of thermophilic bacteria, with isolates found in natural as well as in man-made thermal environments. The high growth rates, cell yields of the cultures, and the constitutive expression of an impressively efficient natural competence apparatus, amongst other properties, make some strains of the genus excellent laboratory models to study the molecular basis of thermophilia. These properties, together with the fact that enzymes and protein complexes from extremophiles are easier to crystallize have led to the development of an ongoing structural biology program dedicated to T. thermophilus HB8, making this organism probably the best so far known from a protein structure point view. Furthermore, the availability of plasmids and up to four thermostable antibiotic selection markers allows its use in physiological studies as a model for ancient bacteria. Regarding biotechnological applications this genus continues to be a source of thermophilic enzymes of great biotechnological interest and, more recently, a tool for the over-expression of thermophilic enzymes or for the selection of thermostable mutants from mesophilic proteins by directed evolution. In this article, we review the properties of this organism as biological model and its biotechnological applications.
Hiromi Kirino - One of the best experts on this subject based on the ideXlab platform.
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molecular cloning and nucleotide sequence of 3 isopropylmalate dehydrogenase gene leub from an extreme thermophile Thermus aquaticus yt 1
Journal of Biochemistry, 1991Co-Authors: Hiromi KirinoAbstract:: A gene (leuB) coding for 3-isopropylmalate dehydrogenase [EC 1.1.1.85] from an extreme thermophile, Thermus aquaticus YT-1 was cloned in Escherichia coli and the nucleotide sequence was determined. It contains an open reading frame of 1,035 bp encoding 344 amino acid residues. The homology with that from T. thermophilus HB8 is 87.0% in nucleotide and 91.3% in amino acid sequences. No overlapped gene was found in the present leuB gene, in contrast to the previous prediction that Thermus leuD gene is overlapped with leuB [Croft et al. (1987) Mol. Gen. Genet. 210, 490-497]. Substitutions in the primary structure which are unique for the thermophile sequences are discussed in relation to the unusual stability of the thermophile dehydrogenase based on amino acid sequence comparison of 9 microorganisms including thermophiles and mesophiles.
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molecular cloning and nucleotide sequence of 3 isopropylmalate dehydrogenase gene leub from an extreme thermophile Thermus aquaticus yt 1
Journal of Biochemistry, 1991Co-Authors: Hiromi KirinoAbstract:: A gene (leuB) coding for 3-isopropylmalate dehydrogenase [EC 1.1.1.85] from an extreme thermophile, Thermus aquaticus YT-1 was cloned in Escherichia coli and the nucleotide sequence was determined. It contains an open reading frame of 1,035 bp encoding 344 amino acid residues. The homology with that from T. thermophilus HB8 is 87.0% in nucleotide and 91.3% in amino acid sequences. No overlapped gene was found in the present leuB gene, in contrast to the previous prediction that Thermus leuD gene is overlapped with leuB [Croft et al. (1987) Mol. Gen. Genet. 210, 490-497]. Substitutions in the primary structure which are unique for the thermophile sequences are discussed in relation to the unusual stability of the thermophile dehydrogenase based on amino acid sequence comparison of 9 microorganisms including thermophiles and mesophiles.
Seiki Kuramitsu - One of the best experts on this subject based on the ideXlab platform.
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Thermostable repair enzyme for oxidative DNA damage from extremely thermophilic bacterium,
1997Co-Authors: Tsutomu Mikawa, Ryuichi Kato, Mitsuaki Sugahara, Seiki KuramitsuAbstract:The mutM (fpg) gene, which encodes a DNA glycosylase that excises an oxidatively damaged form of guanine, was cloned from an extremely thermophilic bacterium, Thermus thermophilus HB8. Its nucleotide sequence encoded a 266 amino acid protein with a molecular mass of ∼30 kDa. Its predicted amino acid sequence showed 42 % identity with the Escherichia coli protein. The amino acid residues Cys, Asn, Gln and Met, known to be chemically unstable at high temperatures, were decreased in number in T.thermophilus MutM protein compared to those of the E.coli one, whereas the number of Pro residues, considered to increase protein stability, was increased. The T.thermophilus mutM gene complemented the mutability of the E.coli mutM mutY double mutant, suggesting that T.thermophilus MutM protein was active in E.coli. The T.thermophilus MutM protein was overproduced in E.coli and then purified to homogeneity. Size-exclusion chromatography indicated that T.thermophilus MutM protein exists as a more compact monomer than the E.coli MutM protein in solution. Circular dichroism measurements indicated that the α-helical content of the protein was ∼30%. Thermus thermophilus MutM protein was stable up to 75C at neutral pH, and between pH 5 and 11 and in the presence of up to 4 M urea at 25C. Denaturation analysis of T.thermophilus MutM protein in the presence of urea suggested that the protein had at least two domains, with estimated stabilities of 8.6 and 16.2 kcal/ mol–1, respectively. Thermus thermophilus MutM protein showed 8-oxoguanine DNA glycosylase activity in vitro at both low and high temperatures
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Mismatch DNA Recognition Protein from an Extremely Thermophilic Bacterium, Thermus Thermophilus HB8
Nucleic Acids Research, 1996Co-Authors: Satoko Takamatsu, Ryuichi Kato, Seiki KuramitsuAbstract:The mutS gene, implicated in DNA mismatch repair, was cloned from an extremely thermophilic bacterium, Thermus thermophilus HB8. Its nucleotide sequence encoded a 819-amino acid protein with a molecular mass of 91.4 kDa. Its predicted amino acid sequence showed 56 and 39% homology with Escherichia coli MutS and human hMsh2 proteins, respectively. The T.thermophilus mutS gene complemented the hypermutability of the E.coli mutS mutant, suggesting that T.thermophilus MutS protein was active in E.coli and could interact with E.coli MutL and/or MutH proteins. The T.thermophilus mutS gene product was overproduced in E.coli and then purified to homogeneity. Its molecular mass was estimated to be 91 kDa by SDS-PAGE but approx. 330 kDa by size-exclusion chromatography, suggesting that T.thermophilus MutS protein was a tetramer in its native state. Circular dichroic measurements indicated that this protein had an alpha-helical content of approx. 50%, and that it was stable between pH 1.5 and 12 at 25 degree C and was stable up to 80 degree C at neutral pH. Thermus thermophilus MutS protein hydrolyzed ATP to ADP and Pi, and its activity was maximal at 80 degrees C. The kinetic parameters of the ATPase activity at 65 degrees C were Km = 130 microM and Kcat = 0.11 s(-1). Thermus thermophilus MutS protein bound specifically with G-T mismatched DNA even at 60 degrees C.
Rosa Martinezarias - One of the best experts on this subject based on the ideXlab platform.
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the genome sequence of the extreme thermophile Thermus thermophilus
Nature Biotechnology, 2004Co-Authors: Anke Henne, Holger Bruggemann, Carsten Raasch, Arnim Wiezer, Thomas Hartsch, Andre Johann, Tanja Lienard, Olivia Gohl, Heiko Liesegang, Rosa MartinezariasAbstract:Thermus thermophilus HB27 is an extremely thermophilic, halotolerant bacterium, which was originally isolated from a natural thermal environment in Japan. This organism has considerable biotechnological potential; many thermostable proteins isolated from members of the genus Thermus are indispensable in research and in industrial applications. We present here the complete genome sequence of T. thermophilus HB27, the first for the genus Thermus. The genome consists of a 1,894,877 base pair chromosome and a 232,605 base pair megaplasmid, designated pTT27. The 2,218 identified putative genes were compared to those of the closest relative sequenced so far, the mesophilic bacterium Deinococcus radiodurans. Both organisms share a similar set of proteins, although their genomes lack extensive synteny. Many new genes of potential interest for biotechnological applications were found in T. thermophilus HB27. Candidates include various proteases and key enzymes of other fundamental biological processes such as DNA replication, DNA repair and RNA maturation.
Kentaro Miyazaki - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequences of Thermus thermophilus strains hb5002 and hb5008 isolated from mine hot spring in japan
Microbiology Resource Announcements, 2021Co-Authors: Kentaro Miyazaki, Toshiyuki Moriya, Tairo Oshima, Kei Yura, Natsuko Tokito, Yoshitaka BesshoAbstract:We isolated Thermus thermophilus strains HB5002 and HB5008 from Mine Hot Spring in Japan. Whole-genome sequencing revealed that they showed ∼100% average nucleotide identity to each other, ≥98.53% to the T. thermophilus strains originating from the same spot but ≤97.64% to the T. thermophilus strains from geographically different places in Japan.
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complete genome sequence of Thermus thermophilus strain hb5018 isolated from mine hot spring in japan
Microbiology Resource Announcements, 2021Co-Authors: Kentaro Miyazaki, Toshiyuki Moriya, Naoki Nemoto, Tairo Oshima, Kei Yura, Yoshitaka BesshoAbstract:ABSTRACT We isolated Thermus thermophilus strain HB5018 from Mine Hot Spring in Japan, where the type strain HB8 was isolated nearly half a century ago. The complete genome sequence of HB5018 showed 99.1% average nucleotide identity with HB8, suggesting strict species conservation in the habitat over the past 50 years.
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complete genome sequencing of Thermus thermophilus strain hc11 isolated from mine geyser in japan
Microbiology resource announcements, 2019Co-Authors: Kentaro MiyazakiAbstract:ABSTRACT Thermus thermophilus strain HC11 was isolated from Mine Geyser in Japan, where type strain HB8 was isolated 50 years ago. In this article, the complete genome sequence of HC11 is presented. HC11 shares the highest average nucleotide identity with HB8 among known T. thermophilus genomes (93.1%) with no genetic rearrangements.
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complete genome sequences of Thermus thermophilus strains aa2 20 and aa2 29 isolated from arima onsen in japan
Microbiology Resource Announcements, 2019Co-Authors: Kentaro Miyazaki, Natsuki TomariguchiAbstract:We isolated halophilic and thermophilic Thermus thermophilus strains AA2-20 and AA2-29 from nonvolcanic, oceanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequences of these organisms to gain insights into halophilicity.
