scholarly journals Three novel canine papillomaviruses support taxonomic clade formation

2009 ◽  
Vol 90 (11) ◽  
pp. 2615-2621 ◽  
Author(s):  
Christian E. Lange ◽  
Kurt Tobler ◽  
Mathias Ackermann ◽  
Lucia Panakova ◽  
Keith L. Thoday ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Human Papillomaviruses ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Whole Genomes ◽  
Sequence Elements ◽  
Sequence Similarities

More than 100 human papillomaviruses (HPVs) have been identified and had their whole genomes sequenced. Most of these HPVs can be classified into three distinct genera, the alpha-, beta- and gamma-papillomaviruses (PVs). Of note, only one or a small number of PVs have been identified for each individual animal species. However, four canine PVs (CPVs) (COPV, CPV2, CPV3 and CPV4) have been described and their entire genomic sequences have been published. Based on their sequence similarities, they belong to three distinct clades. In the present study, circular viral DNA was amplified from three dogs showing signs of pigmented plaques, endophytic papilloma or in situ squamous cell carcinoma. Analysis of the DNA sequences suggested that these are three novel viruses (CPV5, CPV6 and CPV7) whose genomes comprise all the conserved sequence elements of known PVs. The genomes of these seven CPVs were compared in order properly classify them. Interestingly, phylogenetic analyses, as well as pairwise sequence alignments of the putative amino acid sequences, revealed that CPV5 grouped well with CPV3 and CPV4, whereas CPV7 grouped with CPV2 but neither group fitted with other classified PVs. However, CPV6 grouped with COPV, a lambda-PV. Based on this evidence, allocation of CPVs into three distinct clades could therefore be supported. Thus, similar to HPVs, it might be that the known and currently unknown CPVs are related and form just a few clades or genera.

scholarly journals Comparative Structures and Evolution of Vertebrate Carboxyl Ester Lipase (CEL) Genes and Proteins with a Major Role in Reverse Cholesterol Transport

Cholesterol ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Roger S. Holmes ◽  
Laura A. Cox
Keyword(s):  
Amino Acid ◽  
Phylogenetic Analyses ◽  
Hydrolytic Enzyme ◽  
Gene Families ◽  
Repeat Sequence ◽  
Amino Acid Sequences ◽  
Sequence Alignments ◽  
Tertiary Structures ◽  
Lactating Mammary Gland ◽  
Using Data

Bile-salt activated carboxylic ester lipase (CEL) is a major triglyceride, cholesterol ester and vitamin ester hydrolytic enzyme contained within pancreatic and lactating mammary gland secretions. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for CEL genes, and encoded proteins using data from several vertebrate genome projects. A proline-rich and O-glycosylated 11-amino acid C-terminal repeat sequence (VNTR) previously reported for human and other higher primate CEL proteins was also observed for other eutherian mammalian CEL sequences examined. In contrast, opossum CEL contained a single C-terminal copy of this sequence whereas CEL proteins from platypus, chicken, lizard, frog and several fish species lacked the VNTR sequence. Vertebrate CEL genes contained 11 coding exons. Evidence is presented for tandem duplicated CEL genes for the zebrafish genome. Vertebrate CEL protein subunits shared 53–97% sequence identities; demonstrated sequence alignments and identities for key CEL amino acid residues; and conservation of predicted secondary and tertiary structures with those previously reported for human CEL. Phylogenetic analyses demonstrated the relationships and potential evolutionary origins of the vertebrate CEL family of genes which were related to a nematode carboxylesterase (CES) gene and five mammalian CES gene families.

scholarly journals Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Hauke Voß ◽  
Carina Amata Heck ◽  
Marcus Schallmey ◽  
Anett Schallmey
Keyword(s):  
Biochemical Characterization ◽  
Phylogenetic Analyses ◽  
Sequence Motifs ◽  
Database Mining ◽  
Sequence Alignments ◽  
Renewable Source ◽  
Aromatic Polymer ◽  
Conserved Sequence ◽  
Peptide Pattern ◽  
Lignin Depolymerization

ABSTRACT Lignin is the most abundant aromatic polymer in nature and a promising renewable source for the provision of aromatic platform chemicals and biofuels. β-Etherases are enzymes with a promising potential for application in lignin depolymerization due to their selectivity in the cleavage of β-O-4 aryl ether bonds. However, only a very limited number of these enzymes have been described and characterized so far. Using peptide pattern recognition (PPR) as well as phylogenetic analyses, 96 putatively novel β-etherases have been identified, some even originating from bacteria outside the order Sphingomonadales. A set of 13 diverse enzymes was selected for biochemical characterization, and β-etherase activity was confirmed for all of them. Some enzymes displayed up to 3-fold higher activity than previously known β-etherases. Moreover, conserved sequence motifs specific for either LigE- or LigF-type enzymes were deduced from multiple-sequence alignments and the PPR-derived peptides. In combination with structural information available for the β-etherases LigE and LigF, insight into the potential structural and/or functional role of conserved residues within these sequence motifs is provided. Phylogenetic analyses further suggest the presence of additional bacterial enzymes with potential β-etherase activity outside the classical LigE- and LigF-type enzymes as well as the recently described heterodimeric β-etherases. IMPORTANCE The use of biomass as a renewable source and replacement for crude oil for the provision of chemicals and fuels is of major importance for current and future societies. Lignin, the most abundant aromatic polymer in nature, holds promise as a renewable starting material for the generation of required aromatic structures. However, a controlled and selective lignin depolymerization to yield desired aromatic structures is a very challenging task. In this regard, bacterial β-etherases are especially interesting, as they are able to cleave the most abundant bond type in lignin with high selectivity. With this study, we significantly expanded the toolbox of available β-etherases for application in lignin depolymerization and discovered more active as well as diverse enzymes than previously known. Moreover, the identification of further β-etherases by sequence database mining in the future will be facilitated considerably through our deduced etherase-specific sequence motifs.

Parental origin and genome evolution of several Eurasian hexaploid species of Chenopodium (Chenopodiaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (3) ◽  
pp. 163 ◽  
Author(s):  
BOZENA KOLANO ◽  
JAMIE McCANN ◽  
MAJA OSKĘDRA ◽  
MARCELINA CHRAPEK ◽  
MAGDALENA ROJEK ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
5S Rdna ◽  
The Other ◽  
Parental Origin ◽  
B Genome ◽  
Rdna Loci ◽  
History Of ◽  
35S Rdna

Hybridization and polyploidization appear to be ubiquitous in the evolution of Chenopodium s.s., but the origin and the evolutionary history of the polyploid chenopods is still poorly understood. Phylogenetic analyses of DNA sequences of nrITS, four plastid regions, and 5S rDNA spacer region (NTS) of five Eurasian hexaploid chenopods (2n = 6x = 54), C. album, C. giganteum, C. pedunculare C. formosanum and C. opulifolium, and their diploid and tetraploid relatives as well as genomic in situ hybridization (GISH) indicate their allohexaploid origin. The origin of all the analyzed hexaploids have been inferred to have involved B-genome diploid. The identity of the other parent/parents is more elusive. In the case of C. album, C. giganteum and C. pedunculare the second maternal parent seems to be similar to extant C. strictum or C. striatiforme or Asian diploids (e.g. C. acuminatum). In genomes of allohexaploid C. album, C. giganteum and C. pedunculare half of the rDNA were located in the chromosomes of B-subgenome. The remaining rDNA loci were placed in chromosomes originating from the other parent/parents. Although 35S rDNA loci inherited from two parental species seems to be present in these hexaploids, only one ribotype of nrITS was detected.

scholarly journals A short guide to phylogeny reconstruction

2008 ◽  
Vol 53 (No. 10) ◽  
pp. 442-446 ◽  
Author(s):  
E. Michu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Short Introduction ◽  
Closely Related Species ◽  
Origin And Evolution ◽  
Anatomical Characters

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

scholarly journals Primary sequence of ovomucoid messenger RNA as determined from cloned complementary DNA.

1980 ◽  
Vol 87 (2) ◽  
pp. 480-487 ◽  
Author(s):  
J F Catterall ◽  
J P Stein ◽  
P Kristo ◽  
A R Means ◽  
B W O'Malley
Keyword(s):  
Dna Sequences ◽  
Messenger Rna ◽  
Amino Acid Sequences ◽  
Structural Domains ◽  
Complementary Dna ◽  
Homologous Sequences ◽  
Functional Regions ◽  
Bacterial Plasmids ◽  
Dna Mixture

Ovomucoid messenger RNA (mRNAom) comprises approximately 8% of the total mRNA in the estrogen-stimulated oviduct. The recombinant plasmid pOM100 contained DNA complementary to the 3' end of mRNAom. DNA complementary to the 5' end of mRNAom was obtained from a partially purified preparation of mRNAom by polymerization by reverse transcriptase in the presence of a restriction fragment primer from pOM100. The complementary DNA mixture was amplified by molecular cloning using poly dG/dC tailing to form recombinant bacterial plasmids. Recombinant plasmids containing ovomucoid DNA sequences were selected by in situ hybridization to 32P-labeled pOM100 fragments. The longest plasmid containing ovomucoid DNA sequences was designated pOM502. The complete DNA sequence of both pOM100 and pOM502 was determined. The two plasmids appear to contain sequences complementary to the entire length of mRNAom. The nucleic acid sequence agrees with the known amino acid sequences for both ovomucoid and its N-terminal signal peptide. Highly homologous sequences occur in two regions that coincide with structural domains of the protein. Comparison of the sequence of mRNAom with that for other eucaryotic mRNAs allowed identification of possible functional regions in the mRNA molecule.

Relationships, derived from optimum alignments, among amino acid sequences of plant peroxidases

1992 ◽  
Vol 70 (3) ◽  
pp. 543-556 ◽  
Author(s):  
Hugh Tyson
Keyword(s):  
Amino Acid ◽  
Dna Sequences ◽  
Average Distance ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Distance Measurements ◽  
Plant Peroxidases ◽  
Optimum Alignment ◽  
Sequence Relationships ◽  
Sequence Similarities

The amino acid and (or) DNA sequences of 13 plant peroxidases (EC 1.11.1.7), which include isozymes within species, are currently available in data bases; all have similar lengths of approximately 300 amino acids. Sequence relationships among these 13, plus 2 microbial peroxidases of similar length, were examined. The 15 sequences were compared in all 105 pairwise combinations using optimum alignment procedures. Gap penalties were determined from analysis of penalty change effects. Distances between sequences generated by optimum alignments were analysed by clustering techniques to generate dendrograms. Specific distances, which provided pairwise distance measurements independent of the average distance for a sequence, were used to evaluate sequence similarities; closely related sequences produce closely correlated specific distances. Among the seven plant species, five subgroups were established: (1) horseradish isoperoxidases, (2) turnip and wheat, (3) cucumber and tobacco, (4) potato and tomato, and (5) in which cytochrome c peroxidase showed some similarity to ligninase, but both were only distantly related to plant peroxidases. Horseradish isoperoxidases were related to sequences in subgroups 2, 3, and 4 but resembled subgroups 2 and 3 more closely than 4. Subgroup 2 was more related to 3 than any other. Key words: plant peroxidases, sequence relationships, peroxidase profiles.

scholarly journals Expression of Chlorocatechol 1,2-Dioxygenase and Chlorocatechol 2,3-Dioxygenase Genes in Chlorobenzene-Contaminated Subsurface Samples

2003 ◽  
Vol 69 (3) ◽  
pp. 1372-1376 ◽  
Author(s):  
Albin Alfreider ◽  
Carsten Vogt ◽  
Wolfgang Babel
Keyword(s):  
Phylogenetic Analyses ◽  
Reactor Facility ◽  
Pseudomonas Chlororaphis ◽  
Rt Pcr ◽  
Pcr Products ◽  
Dioxygenase Gene ◽  
Gene Transcripts ◽  
Autochthonous Bacteria ◽  
Sequence Similarities

ABSTRACT In order to evaluate the in situ degradative capabilities of microorganisms in an underground reactor facility housing two flowthrough columns filled with aquifer soil, we examined the distribution and phylogeny of gene transcripts encoding enzymes capable of catalyzing the cleavage of the chlorinated aromatic ring during transformation of the main pollutant, chlorobenzene. Initial biostimulation of the autochthonous bacteria in the originally anaerobic reactor columns was achieved by injecting nitrate and oxygen in the form of H2O2. Two broad-range primer pairs were used for reverse transcriptase PCR (RT-PCR) of partial subunit genes of chlorocatechol 1,2-dioxygenase and catechol 2,3-dioxygenase from RNA directly extracted from different groundwater and aquifer samples. Samples retrieved from the lowermost sections of the reactor columns, which were operated in upflow mode, were positive for the presence of chlorocatechol 1,2-dioxygenase and catechol 2,3-dioxygenase mRNA. On the other hand, chlorocatechol 1,2-dioxygenase RT-PCR products were detected in a larger part of each reactor column, up to a zone 5.5 m above the bottom. Phylogenetic analyses of these chlorocatechol 1,2-dioxygenase sequences clearly separated them into two main clusters, one of which was closely affiliated with the broad-spectrum chlorocatechol 1,2-dioxygenase from Pseudomonas chlororaphis RW71. Analysis of sequences obtained from RT-PCR products amplified with catechol 2,3-dioxygenase primers revealed that their closest relative was the chlorocatechol 2,3-dioxygenase gene cbzE from Pseudomonas putida GJ31 (A. E. Mars, J. Kingma, S. R. Kaschabek, W. Reineke, and D. B. Janssen, J. Bacteriol. 181:1309-1318, 1999), with sequence similarities between 97.8 and 99.0%.

scholarly journals Fungi of quarantine concern for China I: Dothideomycetes

2021 ◽  
Author(s):  
P. Zhao ◽  
P.W. Crous ◽  
L.W. Hou ◽  
W.J. Duan ◽  
L. Cai ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Rapid Identification ◽  
Fungal Species ◽  
New Combination ◽  
Helminthosporium Solani ◽  
Whole Genomes ◽  
The One ◽  
One Fungus One Name ◽  
Current List

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentro­spora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens.

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