scholarly journals Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 446 ◽  
Author(s):  
Karen Ebersohn ◽  
Peter Coetzee ◽  
Louwrens P. Snyman ◽  
Robert Swanepoel ◽  
Estelle H. Venter
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Full Genome Sequence ◽  
African Horse Sickness Virus ◽  
Gene Encoding ◽  
Phylogenetic Characterization ◽  
Next Generation Sequencing Ngs ◽  
High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

scholarly journals Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese PeroxidaseIn Vitro

2019 ◽  
Vol 85 (13) ◽  
Author(s):  
Peter L. Herzog ◽  
Leander Sützl ◽  
Beate Eisenhut ◽  
Daniel Maresch ◽  
Dietmar Haltrich ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Lignin Degradation ◽  
Evolutionary Relationship ◽  
Physiological Role ◽  
Redox Cycling ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Pyranose Oxidase

ABSTRACTPyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacteriumKitasatospora aureofaciens(KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substratesin vitro. A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene fromK. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus,KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds betweenKaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity inKaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCEEstablishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase fromKitasatospora aureofaciensis of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively smallK. aureofaciensproteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.

scholarly journals Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 743-750 ◽  
Author(s):  
L D Fletcher ◽  
J M McDowell ◽  
R R Tidwell ◽  
R B Meagher ◽  
C C Dykstra
Keyword(s):  
Phylogenetic Analysis ◽  
Essential Gene ◽  
Pneumocystis Carinii ◽  
Comparative Sequence Analysis ◽  
Cdna Clones ◽  
Actin Gene ◽  
Gene Encoding ◽  
Actin Protein ◽  
Relationship Of ◽  
High Degree

Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.

scholarly journals Isolation and characterization of canine parvovirus type 2c circulating in Uruguay

2011 ◽  
Vol 41 (8) ◽  
pp. 1436-1440 ◽  
Author(s):  
Andrea Blanc Pintos ◽  
Cecilia Beatriz Negro Larrama ◽  
Eduardo Enrique Reolon Baratta ◽  
Mabel Beatriz Berois Barthe ◽  
Juan Ramón Arbiza Rodonz
Keyword(s):  
Cell Culture ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Gene Encoding ◽  
Partial Sequencing ◽  
Phylogenetic Characterization ◽  
Isolation And Characterization ◽  
Restriction Fragment Length

This research reports the first CPV-2c isolation in cell culture (canine fibroma cell line A-72) in Uruguay. The isolates were obtained from 13 rectal swabs of Uruguayan dogs with parvovirosis. Samples were submitted to PCR with two sets of primers, restriction fragment length polymorphism (RFLP), partial sequencing of the gene encoding for VP2 capsid protein and phylogenetic characterization. The strain isolated was confirmed as CPV-2c. These results contribute to a better knowledge of CPV strains circulating in Uruguay and promote an evaluation of the efficacy of heterologous vaccines used to protect against the circulating strains.

scholarly journals Sequencing, Cloning, and High-Level Expression of the pfp Gene, Encoding a PPi-Dependent Phosphofructokinase from the Extremely Thermophilic EubacteriumDictyoglomus thermophilum

2000 ◽  
Vol 182 (16) ◽  
pp. 4661-4666 ◽  
Author(s):  
Yan-Huai R. Ding ◽  
Ron S. Ronimus ◽  
Hugh W. Morgan
Keyword(s):  
Phylogenetic Analysis ◽  
Cloning And Expression ◽  
High Level Expression ◽  
Gene Encoding ◽  
Thermoproteus Tenax ◽  
High Level ◽  
High Degree ◽  
Dictyoglomus Thermophilum ◽  
Degree Of Similarity

ABSTRACT The sequencing, cloning, and expression of the pfp gene from Dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. A phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from Thermoproteus tenax. The recombinant and native enzymes share a high degree of similarity for most properties examined.

scholarly journals Phylogenetic Analysis of Chlamydia trachomatis Tarp and Correlation with Clinical Phenotype

2010 ◽  
Vol 78 (9) ◽  
pp. 3678-3688 ◽  
Author(s):  
Erika I. Lutter ◽  
Christine Bonner ◽  
Martin J. Holland ◽  
Robert J. Suchland ◽  
Walter E. Stamm ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chlamydia Trachomatis ◽  
Clinical Phenotype ◽  
Evolutionary Relationship ◽  
Actin Binding ◽  
Disease Phenotype ◽  
Sexually Transmitted ◽  
Binding Domains ◽  
High Degree ◽  
Reference Strains

ABSTRACT Chlamydia trachomatis is the leading cause of infectious blindness worldwide and is the most commonly reported pathogen causing sexually transmitted infections. Tarp (translocated actin recruiting phosphoprotein), a type III secreted effector that mediates actin nucleation, is central to C. trachomatis infection. The phylogenetic analysis of tarP from reference strains as well as ocular, genital, and lymphogranuloma venereum (LGV) clinical isolates demonstrated an evolutionary relationship with disease phenotype, with LGV and ocular isolates branched into clades that were separate from the urogenital isolates. The sequence analysis of Tarp indicated a high degree of variability and identified trends within clinical groupings. Tarps from LGV strains contained the highest number of tyrosine-rich repeat regions (up to nine) and the fewest (two) predicted actin binding domains. The converse was noted for Tarp proteins from ocular isolates that contained up to four actin binding domains and as few as one tyrosine-rich repeat region. The results suggest that Tarp is among the few known genes to play a role in C. trachomatis adaptations to specific niches within the host.

scholarly journals Characterization of SFO-1, a Plasmid-Mediated Inducible Class A β-Lactamase from Enterobacter cloacae

1999 ◽  
Vol 43 (2) ◽  
pp. 307-313 ◽  
Author(s):  
Yoshimi Matsumoto ◽  
Matsuhisa Inoue
Keyword(s):  
Klebsiella Oxytoca ◽  
Enterobacter Cloacae ◽  
Gram Negative Bacteria ◽  
Phenotypic Characteristics ◽  
Gene Encoding ◽  
E Coli ◽  
Class A ◽  
Citrobacter Diversus ◽  
High Degree

ABSTRACT Enterobacter cloacae 8009 produced an inducible class A β-lactamase which hydrolyzed cefotaxime efficiently. It also hydrolyzed other β-lactams except cephamycins and carbapenems. The activity was inhibited by clavulanic acid and imipenem. Thebla gene was transferable to Escherichia coliby electroporation of plasmid DNA. The molecular mass of the β-lactamase was 29 kDa and its pI was 7.3. All of these phenotypic characteristics of the enzyme except for inducible production resemble those of some extended-spectrum class A β-lactamases like FEC-1. The gene encoding this β-lactamase was cloned and sequenced. The deduced amino acid sequence of the β-lactamase was homologous to the AmpA sequences of the Serratia fonticola chromosomal enzyme (96%), MEN-1 (78%), Klebsiella oxytoca chromosomal enzymes (77%), TOHO-1 (75%), and FEC-1 (72%). The conserved sequences of class A β-lactamases, including the S-X(T)-X(S)-K motif, in the active site were all conserved in this enzyme. On the basis of the high degree of homology to the β-lactamase of S. fonticola, the enzyme was named SFO-1. The ampR gene was located upstream of the ampA gene, and the AmpR sequence of SFO-1 had homology with the AmpR sequences of the chromosomal β-lactamases from Citrobacter diversus(80%), Proteus vulgaris (68%), and Pseudomonas aeruginosa (60%). SFO-1 was also inducible in E. coli. However, a transformant harboring plasmid without intactampR produced a small amount of β-lactamase constitutively, suggesting that AmpR works as an activator ofampA of SFO-1. This is the first report from Japan describing an inducible plasmid-mediated class A β-lactamase in gram-negative bacteria.

Conservation of the opcL gene encoding the peptidoglycan-associated outer-membrane lipoprotein among representatives of the Burkholderia cepacia complex

2004 ◽  
Vol 53 (5) ◽  
pp. 389-398 ◽  
Author(s):  
Maria Plesa ◽  
Abdelaziz Kholti ◽  
Karen Vermis ◽  
Peter Vandamme ◽  
Stavroula Panagea ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Burkholderia Cepacia ◽  
Sequence Data ◽  
Burkholderia Cenocepacia ◽  
Burkholderia Cepacia Complex ◽  
Gene Encoding ◽  
Burkholderia Multivorans ◽  
Outer Membrane Lipoprotein ◽  
Membrane Lipoprotein ◽  
High Degree

Members of the Burkholderia cepacia complex are Gram-negative β-proteobacteria that are classified into nine genomic species or genomovars. Some representatives of this group of bacteria, such as Burkholderia multivorans (genomovar II) and Burkholderia cenocepacia (genomovar III), are considered to be dangerous pathogens for cystic fibrosis (CF) patients because of their capacity to colonize CF lungs. The opcL gene, which encodes the peptidoglycan-associated outer-membrane lipoprotein (PAL), was detected in the genome of Burkholderia sp. LB 400 by a similarity search that was based on the sequence of the Pseudomonas aeruginosa PAL, OprL. Primers that could amplify part of opcL from B. multivorans LMG 13010T were designed. This PCR fragment was used as a probe for screening of a B. multivorans genomic bank, allowing cloning of the complete opcL gene. The complete opcL gene could be PCR-amplified from DNA from all genomovars. The sequences of these opcL genes showed a high degree of conservation (> 95 %) among different species of the B. cepacia complex. OpcL protein that was purified from B. multivorans LMG 13010T was used to generate mouse polyclonal antisera against OpcL. The OpcL protein could be produced in Escherichia coli and detected in outer-membrane fractions by Western blot. Burkholderia cells were labelled by immunofluorescence staining using antibodies against OpcL, but only after treatment with EDTA and SDS. The opcL gene could be amplified directly from the sputa of 15 CF patients who were known to be colonized by B. cepacia; sequence data derived from the amplicons identified the colonizing strains as B. cenocepacia (genomovar III, n = 14) and B. multivorans (n = 1).

scholarly journals The ompA Gene in Chlamydia trachomatis Differs in Phylogeny and Rate of Evolution from Other Regions of the Genome

2006 ◽  
Vol 74 (1) ◽  
pp. 578-585 ◽  
Author(s):  
Brian W. Brunelle ◽  
George F. Sensabaugh
Keyword(s):  
Chlamydia Trachomatis ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phylogenetic Characterization ◽  
Tissue Tropisms

ABSTRACT Strains of Chlamydia trachomatis are classified into serovars based on nucleotide sequence differences in ompA, the gene that encodes the major outer membrane protein. Phylogenetic characterization of strains based on ompA, however, results in serovar groupings that are inconsistent with the distinguishing features of C. trachomatis pathobiology, e.g., tissue tropisms and disease presentation. We have compared nucleotide sequences at multiple sites distributed around the chlamydial genome from 18 strains representing 16 serovars; sampled regions included genes encoding housekeeping enzymes (totaling 2,073 bp), intergenic noncoding segments (1,612 bp), and a gene encoding a second outer membrane protein (porB; 1,023 bp), with the ompA sequence (1,194 bp) used for reference. These comparative analyses revealed substantial variation in nucleotide substitution patterns among the sampled regions, with average pairwise sequence differences ranging from 0.15% for the housekeeping genes to 12.1% for ompA. Phylogenetic characterization of the sampled genomic sequences yielded a strongly supported tree that divides the strains into groupings consistent with C. trachomatis biology and which has a topology quite distinct from the ompA tree. This phylogenetic incongruity can be accounted for by recombination of the ompA gene between different genomic backgrounds. We found, however, no evidence of recombination within or between any of the sampled regions around the C. trachomatis genome apart from ompA. Parallel analysis of published sequence data on four members of the pmp gene family are consistent with the phylogenetic analyses reported here.

scholarly journals Diversity of Wolbachia Endosymbionts in Heteropteran Bugs

2003 ◽  
Vol 69 (10) ◽  
pp. 6082-6090 ◽  
Author(s):  
Yoshitomo Kikuchi ◽  
Takema Fukatsu
Keyword(s):  
Phylogenetic Analysis ◽  
Fragment Length Polymorphism ◽  
Universal Primers ◽  
Multiple Infections ◽  
Polymorphism Analysis ◽  
Phylogenetic Characterization ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Horizontal Transfers

ABSTRACT An extensive survey of Wolbachia endosymbionts in Japanese terrestrial heteropteran bugs was performed by PCR detection with universal primers for wsp and ftsZ genes of Wolbachia, cloning of the PCR products, restriction fragment length polymorphism analysis of infecting Wolbachia types, and molecular phylogenetic characterization of all the detected Wolbachia strains. Of 134 heteropteran species from 19 families examined, Wolbachia infection was detected in 47 species from 13 families. From the 47 species, 59 Wolbachia strains were identified. Of the 59 strains, 16 and 43 were assigned to A group and B group in the Wolbachia phylogeny, respectively. The 47 species of Wolbachia-infected bugs were classified into 8 species with A infection, 28 species with B infection, 2 species with AA infection, 3 species with AB infection, 5 species with BB infection, and 1 species with ABB infection. Molecular phylogenetic analysis showed little congruence between Wolbachia phylogeny and host systematics, suggesting frequent horizontal transfers of Wolbachia in the evolutionary course of the Heteroptera. The phylogenetic analysis also revealed several novel lineages of Wolbachia. Based on statistical analyses of the multiple infections, we propose a hypothetical view that, in the heteropteran bugs, interactions between coinfecting Wolbachia strains are generally not intense and that Wolbachia coinfections have been established through a stochastic process probably depending on occasional horizontal transfers.

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