scholarly journals Hyperthermophilic Thermotoga Species Differ with Respect to Specific Carbohydrate Transporters and Glycoside Hydrolases

2012 ◽  
Vol 78 (6) ◽  
pp. 1978-1986 ◽  
Author(s):  
Andrew D. Frock ◽  
Steven R. Gray ◽  
Robert M. Kelly
Keyword(s):  
Glucose Transporter ◽  
Open Reading Frames ◽  
The Other ◽  
Glycoside Hydrolases ◽  
Phosphotransferase System ◽  
Separate Species ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Sugar Transporters ◽  
Distinguishing Features

ABSTRACTFour hyperthermophilic members of the bacterial genusThermotoga(T. maritima,T. neapolitana,T. petrophila, andThermotogasp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species.T. maritimaandT. neapolitanaexhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose.Thermotogasp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome.T. petrophilaused glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose forT. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the otherThermotogaspecies. This suggested thatT. petrophilaacquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other threeThermotogaspecies. The results here show that subtle differences exist among the hyperthermophilicThermotogaleswith respect to carbohydrate utilization, which supports their designation as separate species.

scholarly journals Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Yuki Saito ◽  
Akira Shigehisa ◽  
Yohei Watanabe ◽  
Naoki Tsukuda ◽  
Kaoru Moriyama-Ohara ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

scholarly journals Genotypic and Phenotypic Evaluation of the Evolution of High-Level Daptomycin Nonsusceptibility in Vancomycin-Resistant Enterococcus faecium

2012 ◽  
Vol 56 (11) ◽  
pp. 6051-6053 ◽  
Author(s):  
Romney M. Humphries ◽  
Theodoros Kelesidis ◽  
Ryan Tewhey ◽  
Warren E. Rose ◽  
Nicholas Schork ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Open Reading Frames ◽  
Vancomycin Resistant Enterococcus ◽  
Single Nucleotide Variants ◽  
Phosphotransferase System ◽  
Single Nucleotide ◽  
Content Type ◽  
Vancomycin Resistant ◽  
High Level ◽  
Reading Frames

ABSTRACTWhole-genome sequencing and cell membrane studies of three clonalEnterococcus faeciumstrains with daptomycin MICs of 4, 32, and 192 μg/ml were performed, revealing nonsynonymous single nucleotide variants in eight open reading frames, including those predicted to encode a phosphoenolpyruvate-dependent, mannose-specific phosphotransferase system, cardiolipin synthetase, and EzrA. Membrane studies revealed a higher net surface charge among the daptomycin-nonsusceptible isolates and increased septum formation in the isolate with a daptomycin MIC of 192 μg/ml.

scholarly journals Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

2013 ◽  
Vol 79 (12) ◽  
pp. 3724-3733 ◽  
Author(s):  
Frank O. Aylward ◽  
Bradon R. McDonald ◽  
Sandra M. Adams ◽  
Alejandra Valenzuela ◽  
Rebeccah A. Schmidt ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Glycoside Hydrolases ◽  
Content Type ◽  
Metabolic Versatility ◽  
Plasmid Recombination ◽  
Environmental Adaptations ◽  
Species Specific

ABSTRACTSphingomonads comprise a physiologically versatile group within theAlphaproteobacteriathat includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm thatSphingomonas,Sphingobium,Sphingopyxis, andNovosphingobiumare well-resolved monophyletic groups with the exception ofSphingomonassp. strain SKA58, which we propose belongs to the genusSphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

scholarly journals Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences

2009 ◽  
Vol 75 (24) ◽  
pp. 7718-7724 ◽  
Author(s):  
Amy L. VanFossen ◽  
Marcel R. A. Verhaart ◽  
Servé M. W. Kengen ◽  
Robert M. Kelly
Keyword(s):  
Transcriptional Response ◽  
Thermophilic Bacterium ◽  
Open Reading Frames ◽  
Transport Systems ◽  
Response Analysis ◽  
Growth Substrate ◽  
Phosphotransferase System ◽  
Carbohydrate Utilization ◽  
Caldicellulosiruptor Saccharolyticus ◽  
Substrate Preferences

ABSTRACT Coutilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on individual monosaccharides (arabinose, fructose, galactose, glucose, mannose, and xylose), mixtures of these sugars, as well as on xylan and xylogluco-oligosacchrides. C. saccharolyticus grew at approximately the same rate (t d, ∼95 min) and to the same final cell density (1 × 108 to 3 × 108 cells/ml) on all sugars and sugar mixtures tested. In the monosaccharide mixture, although simultaneous consumption of all monosaccharides was observed, not all were utilized to the same extent (fructose > xylose/arabinose > mannose/glucose/galactose). Transcriptome contrasts for monosaccharide growth revealed minimal changes in some cases (e.g., 32 open reading frames [ORFs] changed ≥2-fold for glucose versus galactose), while substantial changes occurred for cases involving mannose (e.g., 353 ORFs changed ≥2-fold for glucose versus mannose). Evidence for catabolite repression was not noted for either growth on multisugar mixtures or the corresponding transcriptomes. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for most of the 24 putative carbohydrate ATP-binding cassette transporters and single phosphotransferase system identified in C. saccharolyticus. Although most transporter genes responded to individual monosaccharides and polysaccharides, the genes Csac_0692 to Csac_0694 were upregulated only in the monosaccharide mixture. The results presented here affirm the broad growth substrate preferences of C. saccharolyticus on carbohydrates representative of lignocellulosic biomass and suggest that this bacterium holds promise for biofuel applications.

scholarly journals Investigating the Function of an Arabinan Utilization Locus Isolated from a Termite Gut Community

2014 ◽  
Vol 81 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Grégory Arnal ◽  
Géraldine Bastien ◽  
Nelly Monties ◽  
Anne Abot ◽  
Véronique Anton Leberre ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Plant Biomass ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Glycoside Hydrolases ◽  
Functional Screening ◽  
Content Type ◽  
Termite Gut ◽  
Pentose Sugar

ABSTRACTBiocatalysts are essential for the development of bioprocesses efficient for plant biomass degradation. Previously, a metagenomic clone containing DNA from termite gut microbiota was pinpointed in a functional screening that revealed the presence of arabinofuranosidase activity. Subsequent genetic and bioinformatic analysis revealed that the DNA fragment belonged to a member of the genusBacteroidesand encoded 19 open reading frames (ORFs), and annotation suggested the presence of hypothetical transporter and regulator proteins and others involved in the catabolism of pentose sugar. In this respect and considering the phenotype of the metagenomic clone, it was noted that among the ORFs, there are four putative arabinose-specific glycoside hydrolases, two from family GH43 and two from GH51. In this study, a thorough bioinformatics analysis of the metagenomic clone gene cluster has been performed and the four aforementioned glycoside hydrolases have been characterized. Together, the results provide evidence that the gene cluster is a polysaccharide utilization locus dedicated to the breakdown of the arabinan component in pectin and related substrates. Characterization of the two GH43 and the two GH51 glycoside hydrolases has revealed that each of these enzymes displays specific catalytic capabilities and that when these are combined the enzymes act synergistically, increasing the efficiency of arabinan degradation.

scholarly journals Phosphoenolpyruvate Phosphotransferase System Components Modulate Gene Transcription and Virulence of Borrelia burgdorferi

2015 ◽  
Vol 84 (3) ◽  
pp. 754-764 ◽  
Author(s):  
Bijay K. Khajanchi ◽  
Evelyn Odeh ◽  
Lihui Gao ◽  
Mary B. Jacobs ◽  
Mario T. Philipp ◽  
...  
Keyword(s):  
Borrelia Burgdorferi ◽  
Adenylate Cyclase ◽  
Glucose Transporter ◽  
Phosphotransferase System ◽  
Content Type ◽  
Mouse Infection ◽  
Tick Transmission ◽  
Regulatory Effects ◽  
Gram Negative Organisms

The phosphoenolpyruvate phosphotransferase system (PEP-PTS) and adenylate cyclase (AC) IV (encoded by BB0723 [cyaB]) are well conserved in different species ofBorrelia. However, the functional roles of PEP-PTS and AC in the infectious cycle ofBorreliahave not been characterized previously. We examined 12 PEP-PTS transporter component mutants by needle inoculation of mice to assess their ability to cause mouse infection. Transposon mutants with mutations in the EIIBC components (ptsG) (BB0645, thought to be involved in glucose-specific transport) were unable to cause infection in mice, while all other tested PEP-PTS mutants retained infectivity. Infectivity was partially restored in an intrans-complemented strain of theptsGmutant. While theptsGmutant survived normally in unfed as well as fed ticks, it was unable to cause infection in mice by tick transmission, suggesting that the function ofptsGis essential to establish infection by either needle inoculation or tick transmission. In Gram-negative organisms, the regulatory effects of the PEP-PTS are mediated by adenylate cyclase and cyclic AMP (cAMP) levels. A recombinant protein encoded byB. burgdorferiBB0723 (a putativecyaBhomolog) was shown to have adenylate cyclase activityin vitro; however, mutants with mutations in this gene were fully infectious in the tick-mouse infection cycle, indicating that its function is not required in this process. By transcriptome analysis, we demonstrated that theptsGgene may directly or indirectly modulate gene expression ofBorrelia burgdorferi. Overall, the PEP-PTS glucose transporter PtsG appears to play important roles in the pathogenesis ofB. burgdorferithat extend beyond its transport functions.

scholarly journals Cloning and Sequencing of Inulinase and β-Fructofuranosidase Genes of a Deep-Sea Microbulbifer Species and Properties of Recombinant Enzymes

2012 ◽  
Vol 78 (7) ◽  
pp. 2493-2495 ◽  
Author(s):  
Tohru Kobayashi ◽  
Kohsuke Uchimura ◽  
Shigeru Deguchi ◽  
Koki Horikoshi
Keyword(s):  
Deep Sea ◽  
Open Reading Frames ◽  
The Other ◽  
Recombinant Enzymes ◽  
Cloning And Sequencing ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Reading Frames

ABSTRACTAn inulinase-producingMicrobulbifersp. strain, JAM-3301, was isolated from a deep-sea sediment. An inulin operon that contained three open reading frames was cloned and sequenced. Two of the three genes were expressed. One product was an endo-inulinase, and the other was a β-fructofuranosidase. Both enzymes worked together to effectively degrade inulin.

Posterior approach for cervical intramedullary arteriovenous malformation with diffuse-type nidus

1999 ◽  
Vol 91 (1) ◽  
pp. 105-111 ◽  
Author(s):  
Kenji Ohata ◽  
Toshihiro Takami ◽  
Alaa El-Naggar ◽  
Michiharu Morino ◽  
Akimasa Nishio ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Poor Prognosis ◽  
Posterior Approach ◽  
The Other ◽  
Anterior Spinal Artery ◽  
Neural Element ◽  
Feeding Artery ◽  
Diffuse Type ◽  
Content Type ◽  
Fine Print

✓ The treatment of spinal intramedullary arteriovenous malformations (AVMs) with a diffuse-type nidus that contains a neural element poses different challenges compared with a glomus-type nidus. The surgical elimination of such lesions involves the risk of spinal cord ischemia that results from coagulation of the feeding artery that, at the same time, supplies cord parenchyma. However, based on evaluation of the risks involved in performing embolization, together with the frequent occurrence of reperfusion, which necessitates frequent reembolization, the authors consider surgery to be a one-stage solution to a disease that otherwise has a very poor prognosis. Magnetic resonance (MR) imaging revealed diffuse-type intramedullary AVMs in the cervical spinal cords of three patients who subsequently underwent surgery via the posterior approach. The AVM was supplied by the anterior spinal artery in one case and by both the anterior and posterior spinal arteries in the other two cases. In all three cases, a posterior median myelotomy was performed up to the vicinity of the anterior median fissure that divided the spinal cord together with the nidus, and the feeding artery was coagulated and severed at its origin from the anterior spinal artery. In the two cases in which the posterior spinal artery fed the AVM, the feeding artery was coagulated on the dorsal surface of the spinal cord. Neurological outcome improved in one patient and deteriorated slightly to mildly in the other two patients. Postoperative angiography demonstrated complete disappearance of the AVM in all cases. Because of the extremely poor prognosis of patients with spinal intramedullary AVMs, this surgical technique for the treatment of diffuse-type AVMs provides acceptable operative outcome. Surgical intervention should be considered when managing a patient with a diffuse-type intramedullary AVM in the cervical spinal cord.

Islamic hedging for pilgrimage funds: case of Indonesia

2019 ◽  
Vol 11 (3) ◽  
pp. 328-341
Author(s):  
Rifki Ismal ◽  
Nurul Izzati Septiana
Keyword(s):  
Exchange Rate ◽  
The Other ◽  
Exchange Rate Risk ◽  
Content Type ◽  
Other Hand ◽  
Rate Risk ◽  
Risk Identify ◽  
Hajj Season ◽  
The Right ◽  
Very High

Purpose The demand for Saudi Arabian real (SAR) is very high in the pilgrimage (hajj) season while the authority, unfortunately, does not hedge the hajj funds. As such, the hajj funds are potentially exposed to exchange rate risk, which can impact the value of hajj funds and generate extra cost to the pilgrims. The purpose of this paper is to conduct simulations of Islamic hedging for pilgrimage funds to: mitigate and minimize exchange rate risk, identify and recommend the ideal time, amount and tenors of Islamic hedging for hajj funds, estimate cost saving by pursuing Islamic hedging and propose technical and general recommendations for the authority. Design/methodology/approach Forward transaction mechanism is adopted to compute Islamic forward between SAR and Rupiah (Indonesian currency) or IDR. Findings – based on simulations, the paper finds that: the longer the Islamic hedging tenors, the better is the result of Islamic hedging, the decreasing of IDR/USD is the right time to hedge the hajj funds and, on the other hand, the IDR/SAR appreciation is not the right time to hedge the hajj funds. Findings Based on simulations, the paper finds that: the longer the Islamic hedging tenors, the better is the result of Islamic hedging, the decreasing of IDR/USD is the right time to hedge the hajj funds and, on the other hand, the IDR/SAR appreciation is not the right time to hedge the hajj funds. Research limitations/implications The research suggests the authority to (and not to) hedge the hajj fund, depending on economic conditions and market indicators. Even though the assessment is for the Indonesian case, other countries maintaining hajj funds might also learn from this paper. Originality/value To the best of author’s knowledge, this is the first paper in Indonesia that attempts to simulate the optimal hedging of hajj funds.

scholarly journals Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments

2021 ◽  
Author(s):  
Sherlynette Pérez Castro ◽  
Mikayla A. Borton ◽  
Kathleen Regan ◽  
Isabella Hrabe de Angelis ◽  
Kelly C. Wrighton ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Extracellular Enzyme ◽  
Trophic Levels ◽  
Glycoside Hydrolases ◽  
Biological Macromolecules ◽  
Guaymas Basin ◽  
Bacterial Phyla ◽  
Sugar Transporters ◽  
Hydrothermal Sediments ◽  
Thermophilic Conditions

AbstractHydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.

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