scholarly journals Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides

2011 ◽  
Vol 78 (1) ◽  
pp. 242-249 ◽  
Author(s):  
Eun-Mi Kim ◽  
Juhan Kim ◽  
Joo-Hyun Seo ◽  
Jun-Seong Park ◽  
Duck-Hee Kim ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Large Subunit ◽  
Small Subunit ◽  
Compound K ◽  
Oxidation Activity ◽  
Content Type ◽  
Molecular Masses ◽  
Ginsenoside Compound K ◽  
Identification And Characterization

ABSTRACTUsing enrichment culture,Rhizobiumsp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex fromRhizobiumsp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosylation of compound K was performed via oxidation of ginsenoside glucose by glycoside oxidoreductase. Coexpression of the small subunit helped soluble expression of the large subunit in recombinantEscherichia coli. The purified large subunit also showed oxidation activity against other ginsenoside compounds, such as Rb1, Rb2, Rb3, Rc, F2, CK, Rh2, Re, F1, and the isoflavone daidzin, but at a much lower rate. When oxidized CK was extracted and incubated in phosphate buffer with or without enzyme, (S)-protopanaxadiol [PPD(S)] was detected in both cases, which suggests that deglycosylation of oxidized glucose is spontaneous.

Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo

Parasitology ◽  
1999 ◽  
Vol 118 (6) ◽  
pp. 541-551 ◽  
Author(s):  
N. E. COLLINS ◽  
B. A. ALLSOPP
Keyword(s):  
Genetic Recombination ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Gene Pools ◽  
Theileria Parva ◽  
Causative Agents ◽  
Internal Transcribed Spacer Sequences

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5·8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93·5% of T. p. parva isolates examined were detected by probe TPP1 and 81·8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

Identification and characterization of two novel calpain large subunit genes

Gene ◽  
2001 ◽  
Vol 274 (1-2) ◽  
pp. 245-252 ◽  
Author(s):  
T.Neil Dear ◽  
Thomas Boehm
Keyword(s):  
Large Subunit ◽  
Identification And Characterization

scholarly journals Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

2011 ◽  
Vol 78 (2) ◽  
pp. 334-345 ◽  
Author(s):  
Tsvetan R. Bachvaroff ◽  
Sunju Kim ◽  
Laure Guillou ◽  
Charles F. Delwiche ◽  
D. Wayne Coats
Keyword(s):  
Large Subunit ◽  
Small Subunit ◽  
Base Change ◽  
Pcr Analysis ◽  
Ssu Rrna ◽  
Compensatory Base Change ◽  
Content Type ◽  
Single Cell Pcr ◽  
Group I ◽  
Lsu Rrna

ABSTRACTThe genusEuduboscquellais one of a few described genera within the syndinean dinoflagellates, an enigmatic lineage with abundant diversity in marine environmental clone libraries based on small subunit (SSU) rRNA. The region composed of the SSU through to the partial large subunit (LSU) rRNA was determined from 40 individual tintinnid ciliate loricae infected withEuduboscquellasampled from eight surface water sites in the Northern Hemisphere, producing seven distinct SSU sequences. The corresponding host SSU rRNA region was also amplified from eight host species. The SSU tree ofEuduboscquellaand syndinean group I sequences from environmental clones had seven well-supported clades and one poorly supported clade across data sets from 57 to 692 total sequences. The genusEuduboscquellaconsistently formed a supported monophyletic clade within a single subclade of group I sequences. For most parasites with identical SSU sequences, the more variable internal transcribed spacer (ITS) to LSU rRNA regions were polymorphic at 3 to 10 sites. However, inE. cachonithere was variation between ITS to LSU copies at up to 20 sites within an individual, while in a parasite ofTintinnopsisspp., variation between different individuals ranged up to 19 polymorphic sites. However, applying the compensatory base change model to the ITS2 sequences suggested no compensatory changes within or between individuals with the same SSU sequence, while one to four compensatory changes between individuals with similar but not identical SSU sequences were found. Comparisons between host and parasite phylogenies do not suggest a simple pattern of host or parasite specificity.

scholarly journals Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

2014 ◽  
Vol 80 (16) ◽  
pp. 4958-4967 ◽  
Author(s):  
Marjolaine Martin ◽  
Sophie Biver ◽  
Sébastien Steels ◽  
Tristan Barbeyron ◽  
Murielle Jam ◽  
...  
Keyword(s):  
Metagenomic Library ◽  
Functional Screening ◽  
Sample Collection ◽  
Prolonged Incubation ◽  
Content Type ◽  
Cold Active ◽  
Esterase Loci ◽  
Collection Period ◽  
Identification And Characterization

ABSTRACTA metagenomic library was constructed from microorganisms associated with the brown algaAscophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.

scholarly journals A Real-Time PCR Assay for Simultaneous Detection and Differentiation of Four Common Entamoeba Species That Infect Humans

2020 ◽  
Vol 59 (1) ◽  
pp. e01986-20
Author(s):  
Ibne Karim M. Ali ◽  
Shantanu Roy
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Simultaneous Detection ◽  
Small Subunit ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Content Type ◽  
Rdna Sequences ◽  
Appropriate Treatment

ABSTRACTThere are over 40 species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, and yet differentiation is important for appropriate treatment decisions. Here, we developed a hydrolysis probe-based tetraplex real-time PCR assay that can simultaneously detect and differentiate these four species in clinical samples. In this assay, multicopy small-subunit (SSU) ribosomal DNA (rDNA) sequences were used as targets. We determined that the tetraplex real-time PCR can detect amebic DNA corresponding to as little as a 0.1 trophozoite equivalent of any of these species. We also determined that this assay can detect E. histolytica DNA in the presence of 10-fold more DNA from another Entamoeba species in mixed-infection scenarios. With a panel of more than 100 well-characterized clinical samples diagnosed and confirmed using a previously published duplex real-time PCR (capable of detecting E. histolytica and E. dispar), our tetraplex real-time PCR assay demonstrated levels of sensitivity and specificity comparable with those demonstrated by the duplex real-time PCR assay. The advantage of our assay over the duplex assay is that it can specifically detect two additional Entamoeba species and can be used in conventional PCR format. This newly developed assay will allow further characterization of the epidemiology and pathogenicity of the four morphologically identical Entamoeba species, especially in low-resource settings.

scholarly journals Purification and comparison of the structures of human liver acidic α-d-mannosidases A and B

1986 ◽  
Vol 233 (1) ◽  
pp. 65-72 ◽  
Author(s):  
S H Cheng ◽  
S Malcolm ◽  
S Pemble ◽  
B Winchester
Keyword(s):  
Molecular Mass ◽  
Isoelectric Focusing ◽  
Concanavalin A ◽  
Human Liver ◽  
Large Subunit ◽  
Small Subunit ◽  
Single Locus ◽  
Structure And Properties ◽  
Molecular Masses ◽  
High Mannose

Human liver alpha-D-mannosidases A and B were purified 11 500-fold and 2000-fold respectively. Both showed microheterogeneity when analysed by isoelectric focusing. Alpha-D-Mannosidases A and B are immunologically identical but differ in their range of pI values, molecular masses, uptake into fibroblasts and subunit compositions. Alpha-D-Mannosidase A consists of equimolar proportions of subunits of molecular masses 62 kDa and 26 kDa, which are linked by disulphide bridges in the intact enzyme. Alpha-D-Mannosidase B also contains a small subunit, of molecular mass 26 kDa, and a variable mixture of larger subunits, of molecular masses 58 kDa and 62 kDa. The 62 kDa and 58 kDa subunits, but not the 26 kDa one, contain concanavalin A-recognizing glycans. The 58 kDa subunit has a lower pI, contains less high-mannose glycans but probably contains more mannose 6-phosphate than the 62 kDa subunit. It is postulated that the differences in structure and properties of alpha-D-mannosidases A and B are due to differences in the state of processing of the large subunit. This suggestion is consistent with a single locus on chromosome 19 for lysosomal alpha-D-mannosidase.

scholarly journals Tannin Degradation by a Novel Tannase Enzyme Present in Some Lactobacillus plantarum Strains

2014 ◽  
Vol 80 (10) ◽  
pp. 2991-2997 ◽  
Author(s):  
Natalia Jiménez ◽  
María Esteban-Torres ◽  
José Miguel Mancheño ◽  
Blanca de las Rivas ◽  
Rosario Muñoz
Keyword(s):  
Lactobacillus Plantarum ◽  
Tannic Acid ◽  
Plant Material ◽  
Aliphatic Alcohol ◽  
Methyl Gallate ◽  
Content Type ◽  
Sequence Identity ◽  
Tannin Degradation ◽  
Identification And Characterization

ABSTRACTLactobacillus plantarumis frequently isolated from the fermentation of plant material where tannins are abundant.L. plantarumstrains possess tannase activity to degrade plant tannins. AnL. plantarumtannase (TanBLp, formerly called TanLp1) was previously identified and biochemically characterized. In this study, we report the identification and characterization of a novel tannase (TanALp). While all 29L. plantarumstrains analyzed in the study possess thetanBLpgene, the genetanALpwas present in only four strains. Upon methyl gallate exposure, the expression oftanBLpwas induced, whereastanALpexpression was not affected. TanALpshowed only 27% sequence identity to TanBLp, but the residues involved in tannase activity are conserved. Optimum activity for TanALpwas observed at 30°C and pH 6 in the presence of Ca2+ions. TanALpwas able to hydrolyze gallate and protocatechuate esters with a short aliphatic alcohol substituent. Moreover, TanALpwas able to fully hydrolyze complex gallotannins, such as tannic acid. The presence of the extracellular TanALptannase in someL. plantarumstrains provides them an advantage for the initial degradation of complex tannins present in plant environments.

scholarly journals Identification and Characterization of Mycobacterium tuberculosis Beijing Genotype Strain SBH163, Isolated in Sabah, Malaysia

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Jaeyres Jani ◽  
Siti Fatimah Abu Bakar ◽  
Zainal Arifin Mustapha ◽  
Chin Kai Ling ◽  
Roddy Teo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequence ◽  
Beijing Genotype ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Content Type ◽  
Identification And Characterization ◽  
Insight Into ◽  
Malaysian Borneo

This is a report on the whole-genome sequence of Mycobacterium tuberculosis strain SBH163, which was isolated from a patient in the Malaysian Borneo state of Sabah. This report provides insight into the molecular characteristics of an M. tuberculosis Beijing genotype strain related to strains from Russia and South Africa.

scholarly journals Malonic Semialdehyde Reductase from the Archaeon Nitrosopumilus maritimus Is Involved in the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle

2014 ◽  
Vol 81 (5) ◽  
pp. 1700-1707 ◽  
Author(s):  
Julia Otte ◽  
Achim Mall ◽  
Daniel M. Schubert ◽  
Martin Könneke ◽  
Ivan A. Berg
Keyword(s):  
Succinic Semialdehyde ◽  
Alcohol Dehydrogenases ◽  
Content Type ◽  
Metallosphaera Sedula ◽  
Ammonia Oxidizing Archaea ◽  
The Family ◽  
Terrestrial Environments ◽  
Identification And Characterization ◽  
Low Activity

ABSTRACTThe recently described ammonia-oxidizing archaea of the phylumThaumarchaeotaare highly abundant in marine, geothermal, and terrestrial environments. All characterized representatives of this phylum are aerobic chemolithoautotrophic ammonia oxidizers assimilating inorganic carbon via a recently described thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. Although some genes coding for the enzymes of this cycle have been identified in the genomes ofThaumarchaeota, many other genes of the cycle are not homologous to the characterized enzymes from other species and can therefore not be identified bioinformatically. Here we report the identification and characterization of malonic semialdehyde reductase Nmar_1110 in the cultured marine thaumarchaeonNitrosopumilus maritimus. This enzyme, which catalyzes the reduction of malonic semialdehyde with NAD(P)H to 3-hydroxypropionate, belongs to the family of iron-containing alcohol dehydrogenases and is not homologous to malonic semialdehyde reductases fromChloroflexus aurantiacusandMetallosphaera sedula. It is highly specific to malonic semialdehyde (Km, 0.11 mM;Vmax, 86.9 μmol min−1mg−1of protein) and exhibits only low activity with succinic semialdehyde (Km, 4.26 mM;Vmax, 18.5 μmol min−1mg−1of protein). Homologues ofN. maritimusmalonic semialdehyde reductase can be found in the genomes of allThaumarchaeotasequenced so far and form a well-defined cluster in the phylogenetic tree of iron-containing alcohol dehydrogenases. We conclude that malonic semialdehyde reductase can be regarded as a characteristic enzyme for the thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle.

scholarly journals Two Zinc Uptake Systems Contribute to the Full Virulence of Listeria monocytogenes during GrowthIn VitroandIn Vivo

2011 ◽  
Vol 80 (1) ◽  
pp. 14-21 ◽  
Author(s):  
David Corbett ◽  
Jiahui Wang ◽  
Stephanie Schuler ◽  
Gloria Lopez-Castejon ◽  
Sarah Glenn ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Zinc Uptake ◽  
Detectable Effect ◽  
Intracellular Growth ◽  
Content Type ◽  
Zinc Sensing ◽  
Identification And Characterization ◽  
Cell Deletion

ABSTRACTWe report here the identification and characterization of two zinc uptake systems, ZurAM and ZinABC, in the intracellular pathogenListeria monocytogenes. Transcription of both operons was zinc responsive and regulated by the zinc-sensing repressor Zur. Deletion of eitherzurAMorzinAhad no detectable effect on growth in defined media, but a doublezurAM zinAmutant was unable to grow in the absence of zinc supplementation. Deletion ofzinAhad no detectable effect on intracellular growth in HeLa epithelial cells. In contrast, growth of thezurAMmutant was significantly impaired in these cells, indicating the importance of the ZurAM system during intracellular growth. Notably, the deletion of bothzinAandzurAMseverely attenuated intracellular growth, with the double mutant being defective in actin-based motility and unable to spread from cell to cell. Deletion of eitherzurAMorzinAhad a significant effect on virulence in an oral mouse model, indicating that both zinc uptake systems are importantin vivoand establishing the importance of zinc acquisition during infection byL. monocytogenes. The presence of two zinc uptake systems may offer a mechanism by whichL. monocytogenescan respond to zinc deficiency within a variety of environments and during different stages of infection, with each system making distinct contributions under different stress conditions.

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