Pierpaolo Falcicchio, Suzanne Wolterink-Van Loo, Maurice C R Franssen, John van der Oost
{"title":"DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications.","authors":"Pierpaolo Falcicchio, Suzanne Wolterink-Van Loo, Maurice C R Franssen, John van der Oost","doi":"10.1007/s00792-013-0593-x","DOIUrl":"https://doi.org/10.1007/s00792-013-0593-x","url":null,"abstract":"<p><p>Generating new carbon-carbon (C-C) bonds in an enantioselective way is one of the big challenges in organic synthesis. Aldolases are a natural tool for stereoselective C-C bond formation in a green and sustainable way. This review will focus on thermophilic aldolases in general and on dihydroxyacetone phosphate-dependent aldolases in particular. Biochemical properties and applications for synthesis of rare sugars and carbohydrates will be discussed. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"1-13"},"PeriodicalIF":2.9,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0593-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40270030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hua Zhang, Zhenhui Wang, Lei Wang, Ren Mu, Zhi Zou, Kun Yuan, Yuekun Wang, Haiping Wu, Juquan Jiang, Lifu Yang
{"title":"Cloning and identification of a novel NhaD-type Na+/H+ antiporter from metagenomic DNA of the halophilic bacteria in soil samples around Daban Salt Lake.","authors":"Hua Zhang, Zhenhui Wang, Lei Wang, Ren Mu, Zhi Zou, Kun Yuan, Yuekun Wang, Haiping Wu, Juquan Jiang, Lifu Yang","doi":"10.1007/s00792-013-0600-2","DOIUrl":"https://doi.org/10.1007/s00792-013-0600-2","url":null,"abstract":"<p><p>In this study, metagenomic DNA was screened for the Na(+)/H(+) antiporter gene from the halophilic bacteria in Daban Salt Lake by selection in Escherichia coli KNabc lacking three major Na(+)/H(+) antiporters. One gene designated as Hb_nhaD encoding a novel NhaD-type Na(+)/H(+) antiporter was finally cloned. The presence of Hb_NhaD conferred tolerance of E. coli KNabc to up to 0.5 M NaCl and 0.2 M LiCl, and an alkaline pH. Hb_NhaD has the highest identity (70.6%) with a putative NhaD-type Na(+)/H(+) antiporter from an uncharacterized Clostridiaceae species, and also has lower identity with known NhaD-type Na(+)/H(+) antiporters from Halomonas elongata (20.8%), Alkalimonas amylolytica (19.0%), Vibrio parahaemolyticus (18.9%) and Vibrio cholerae (18.7 %). pH-dependent Na(+)(Li(+))/H(+) antiport activity was detected from everted membrane vesicles prepared from E. coli KNabc carrying Hb_nhaD. Hb_NhaD exhibited very high Na(+)(Li(+))/H(+) antiport activity over a wide pH range from 6.5 to 9.0 with the highest activity at pH 7.0 which is significantly different from those of the above known NhaD-type Na(+)/H(+) antiporters. Also, the apparent K m values of Hb_NhaD for Na(+) and Li(+) at pH 7.0 were determined to be 1.31 and 2.16, respectively. Based on the above results, we proposed that Hb_NhaD should be categorized as a novel NhaD-type Na(+)/H(+) antiporter.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"89-98"},"PeriodicalIF":2.9,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0600-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39976661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michael Riis Hansen, Kristine Steen Jensen, Mads Skytte Rasmussen, Stig Christoffersen, Anders Kadziola, Kaj Frank Jensen
{"title":"Specificities and pH profiles of adenine and hypoxanthine-guanine-xanthine phosphoribosyltransferases (nucleotide synthases) of the thermoacidophile archaeon Sulfolobus solfataricus.","authors":"Michael Riis Hansen, Kristine Steen Jensen, Mads Skytte Rasmussen, Stig Christoffersen, Anders Kadziola, Kaj Frank Jensen","doi":"10.1007/s00792-013-0595-8","DOIUrl":"https://doi.org/10.1007/s00792-013-0595-8","url":null,"abstract":"<p><p>Two open reading frames in the genome of Sulfolobus solfataricus (SSO2342 [corrected] and SSO2424) were cloned and expressed in E. coli. The protein products were purified and their enzymatic activity characterized. Although SSO2342 [corrected] was annotated as a gene (gpT-1) encoding a 6-oxopurine phosphoribosyltransferase (PRTase), the protein product turned out to be a PRTase highly specific for adenine and we suggest that the reading frame should be renamed apT. The other reading frame SSO2424 (gpT-2) proved to be a true 6-oxopurine PRTase active with hypoxanthine, xanthine and guanine as substrates, and we suggest that the gene should be renamed gpT. Both enzymes exhibited unusual profiles of activity versus pH. The adenine PRTase showed the highest activity at pH 7.5-8.5, but had a distinct peak of activity also at pH 4.5. The 6-oxo PRTase showed maximal activity with hypoxanthine and guanine around pH 4.5, while maximal activity with xanthine was observed at pH 7.5. We discuss likely reasons why SSO2342 [corrected] in S. solfataricus and similar open reading frames in other Crenarchaeota could not be identified as genes encoding APRTase.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"179-87"},"PeriodicalIF":2.9,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0595-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40266149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Susanne Erdmann, Bo Chen, Xiaoxing Huang, Ling Deng, Chao Liu, Shiraz A Shah, Sven Le Moine Bauer, Carlos León Sobrino, Haina Wang, Yunlin Wei, Qunxin She, Roger A Garrett, Li Huang, Lianbing Lin
{"title":"A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species.","authors":"Susanne Erdmann, Bo Chen, Xiaoxing Huang, Ling Deng, Chao Liu, Shiraz A Shah, Sven Le Moine Bauer, Carlos León Sobrino, Haina Wang, Yunlin Wei, Qunxin She, Roger A Garrett, Li Huang, Lianbing Lin","doi":"10.1007/s00792-013-0591-z","DOIUrl":"https://doi.org/10.1007/s00792-013-0591-z","url":null,"abstract":"<p><p>A newly isolated single-tailed fusiform virus, Sulfolobus tengchongensis spindle-shaped virus STSV2, from Hamazui, China, is characterised. It contains a double-stranded modified DNA genome of 76,107 bp and is enveloped by a lipid membrane structure. Virions exhibit a single coat protein that forms oligomers when isolated. STSV2 is related to the single-tailed fusiform virus STSV1 and, more distantly, to the two-tailed bicaudavirus ATV. The virus can be stably cultured over long periods in laboratory strains of Sulfolobus and no evidence was found for cell lysis under different stress conditions. Therefore, it constitutes an excellent model virus for archaeal virus-host studies. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"51-60"},"PeriodicalIF":2.9,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0591-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40269796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isabel Maida, Marco Fondi, Maria Cristiana Papaleo, Elena Perrin, Valerio Orlandini, Giovanni Emiliani, Donatella de Pascale, Ermenegilda Parrilli, Maria Luisa Tutino, Luigi Michaud, Angelina Lo Giudice, Riccardo Romoli, Gianluca Bartolucci, Renato Fani
{"title":"Phenotypic and genomic characterization of the Antarctic bacterium Gillisia sp. CAL575, a producer of antimicrobial compounds.","authors":"Isabel Maida, Marco Fondi, Maria Cristiana Papaleo, Elena Perrin, Valerio Orlandini, Giovanni Emiliani, Donatella de Pascale, Ermenegilda Parrilli, Maria Luisa Tutino, Luigi Michaud, Angelina Lo Giudice, Riccardo Romoli, Gianluca Bartolucci, Renato Fani","doi":"10.1007/s00792-013-0590-0","DOIUrl":"https://doi.org/10.1007/s00792-013-0590-0","url":null,"abstract":"<p><p>Microorganisms from Antarctica have evolved particular strategies to cope with cold. Moreover, they have been recently reported as producers of antimicrobial compounds, which inhibit the growth of other bacteria. In this work we characterized from different viewpoints the Gillisia sp. CAL575 strain, a psychrotrophic bacterium that produces microbial volatile organic compounds involved in the growth inhibition of Burkholderia cepacia complex members. Sequencing and analysis of the whole genome of Gillisia sp. CAL575 revealed that it includes genes that are involved in secondary metabolite production, adaptation to cold conditions, and different metabolic pathways for the production of energy. All these features make Gillisia sp. CAL575 a possible tool for biotechnology. </p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"35-49"},"PeriodicalIF":2.9,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0590-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40259600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biochemical characterization of two glutamate dehydrogenases with different cofactor specificities from a hyperthermophilic archaeon Pyrobaculum calidifontis.","authors":"Taisuke Wakamatsu, Chisato Higashi, Taketo Ohmori, Katsumi Doi, Toshihisa Ohshima","doi":"10.1007/s00792-013-0527-7","DOIUrl":"https://doi.org/10.1007/s00792-013-0527-7","url":null,"abstract":"<p><p>Two putative glutamate dehydrogenase (GDH) genes (pcal_1031 and pcal_1606) were found in a sulfur-dependent hyperthermophilic archaeon, Pyrobaculum calidifontis. The two genes were then expressed in Escherichia coli, and both of the recombinant gene products showed GDH activity. The two enzymes were then purified to homogeneity and characterized in detail. Although both purified GDHs had a hexameric structure and neither exhibited allosteric regulation, they showed different coenzyme specificities: one was specific for NAD(+), the other for NADP(+) and different heat activation mechanisms. In addition, there was little difference in the kinetic constants, optimal temperature, thermal stability, optimal pH and pH stability between the two enzymes. The overall sequence identity between the two proteins was very high (81%), but was not high in the region recognizing the 2' position of the adenine ribose moiety, which is responsible for coenzyme specificity. This is the first report on the identification of two GDHs with different coenzyme specificities from a single hyperthermophilic archaeon and the definition of their basic in vitro properties.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"379-89"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0527-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31319787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander I Saralov, Roman V Baslerov, Boris B Kuznetsov
{"title":"Haloferax chudinovii sp. nov., a halophilic archaeon from Permian potassium salt deposits.","authors":"Alexander I Saralov, Roman V Baslerov, Boris B Kuznetsov","doi":"10.1007/s00792-013-0534-8","DOIUrl":"https://doi.org/10.1007/s00792-013-0534-8","url":null,"abstract":"<p><p>Three pigmented strains of halophilic archaea (RS75, RS77, RS79) were isolated from the monoliths of mottled sylvinite from the Verkhnekamsk salt deposit (Solikamsk, Russia). The cells were nonmotile, gram-negative, pleomorphic, disk-shaped or ovoid, 0.8-1.0 × 1.5-2.5 μm. The organism was a chemoorganotrophic obligate aerobe producing catalase and oxidase. A number of carbohydrates and carboxylic acids were used as growth substrates. Growth occurred in the presence of 7-27% NaCl (with the optimum at 15-18%), 0.02-20% KCl (0.2-1%), 0.2-16% MgCl2 (2-3%), in the temperature range from 23 to 51 °C (40-45 °C), and pH 5.5-8.0 (6.8-7.0). The membranes contained carotenoids of the bacterioruberin series. Phosphatidylglyceromethylphosphate (PGP-Me), phosphatidylglycerol (PG), sulfated diglycosyl diether (S-DGD-1) predominated among the polar lipids. The DNA G + C content was 64.0-65.0 mol %. Phylogenetic analysis of the 16S rRNA gene sequences showed high similarity of the new strains to Haloferax species: H. denitrificans (99.2%) and H. volcanii (99.1%), H. larsenii (96.9%) and H. elongans (96.6%). DNA-DNA hybridization revealed 93-95% similarity between strain RS75 and strains RS77 and RS79; the similarity levels between strain RS75 and the type strains of Haloferax denitrificans VKM B-1754(T) and Halobacterium salinarum VKM B-1769(T) were 50 and 10%, respectively. According to its phenotypic and genotypic characteristics, the organism was classified as a member of the genus Haloferax, forming a new species with the proposed name Haloferax chudinovii sp. nov. type strain is RS75(T) (=VKPM B-11279(T)).</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"499-504"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0534-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31333961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cristian Coman, Bogdan Drugă, Adriana Hegedus, Cosmin Sicora, Nicolae Dragoş
{"title":"Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania.","authors":"Cristian Coman, Bogdan Drugă, Adriana Hegedus, Cosmin Sicora, Nicolae Dragoş","doi":"10.1007/s00792-013-0537-5","DOIUrl":"https://doi.org/10.1007/s00792-013-0537-5","url":null,"abstract":"<p><p>The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"523-34"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0537-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31435053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unique substrate specificity of purine nucleoside phosphorylases from Thermus thermophilus.","authors":"Fumiaki Tomoike, Seiki Kuramitsu, Ryoji Masui","doi":"10.1007/s00792-013-0535-7","DOIUrl":"https://doi.org/10.1007/s00792-013-0535-7","url":null,"abstract":"<p><p>The degradation of purine nucleoside is the first step of purine nucleoside uptake. This degradation is catalyzed by purine nucleoside phosphorylase, which is categorized into two classes: hexameric purine nucleoside phosphorylase (6PNP) and trimeric purine nucleoside phosphorylase (3PNP). Generally, 6PNP and 3PNP degrade adenosine and guanosine, respectively. However, the substrate specificity of 6PNP and 3PNP of Thermus thermophilus (tt6PNP and tt3PNP, respectively) is the reverse of that anticipated based on comparison to other phosphorylases. Specifically, in this paper we reveal by gene disruption that tt6PNP and tt3PNP are discrete enzymes responsible for the degradation of guanosine and adenosine, respectively, in T. thermophilus HB8 cells. Sequence comparison combined with structural information suggested that Asn204 in tt6PNP and Ala196/Asp238 in tt3PNP are key residues for defining their substrate specificity. Replacement of Asn204 in tt6PNP with Asp changed the substrate specificity of tt6PNP to that of a general 6PNP. Similarly, substitution of Ala196 by Glu and Asp238 by Asn changed the substrate specificity of tt3PNP to that of a general 3PNP. Our results indicate that the residues at these positions determine substrate specificity of PNPs in general. Sequence analysis further suggested most 6PNP and 3PNP enzymes in thermophilic species belonging to the Deinococcus-Thermus phylum share the same critical residues as tt6PNP and tt3PNP, respectively.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"505-14"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0535-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40241544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lukasz Dziewit, Adrian Cegielski, Krzysztof Romaniuk, Witold Uhrynowski, Antoni Szych, Pawel Niesiobedzki, Magdalena J Zmuda-Baranowska, Marek K Zdanowski, Dariusz Bartosik
{"title":"Plasmid diversity in arctic strains of Psychrobacter spp.","authors":"Lukasz Dziewit, Adrian Cegielski, Krzysztof Romaniuk, Witold Uhrynowski, Antoni Szych, Pawel Niesiobedzki, Magdalena J Zmuda-Baranowska, Marek K Zdanowski, Dariusz Bartosik","doi":"10.1007/s00792-013-0521-0","DOIUrl":"https://doi.org/10.1007/s00792-013-0521-0","url":null,"abstract":"<p><p>Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments.</p>","PeriodicalId":288153,"journal":{"name":"Extremophiles : life under extreme conditions","volume":" ","pages":"433-44"},"PeriodicalIF":2.9,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00792-013-0521-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31389297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}