Cloning, Expression, and Characterization of acis-3-Chloroacrylic Acid Dehalogenase:  Insights into the Mechanistic, Structural, and Evolutionary Relationship between Isomer-Specific 3-Chloroacrylic Acid Dehalogenases†

Biochemistry ◽  
2004 ◽  
Vol 43 (3) ◽  
pp. 759-772 ◽  
Author(s):  
Gerrit J. Poelarends ◽  
Hector Serrano ◽  
Maria D. Person ◽  
William H. Johnson, ◽  
Alexey G. Murzin ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Chloroacrylic Acid Dehalogenase

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.

The disparity of the Burgess Shale arthropod fauna and the limits of cladistic analysis: why we must strive to quantify morphospace

Paleobiology ◽  
1991 ◽  
Vol 17 (4) ◽  
pp. 411-423 ◽  
Author(s):  
Stephen Jay Gould
Keyword(s):  
Evolutionary Relationship ◽  
Cladistic Analysis ◽  
Difficult Problem ◽  
High Rank ◽  
Burgess Shale ◽  
Taxonomic Rank ◽  
Arthropod Fauna ◽  
Active Stabilization ◽  
History Of

Three major arguments have been raised against the crucial claim, documented by Whittington and colleagues for the Burgess Shale fauna, and so contrary to traditional views, that disparity of anatomical design reached an early maximum in the history of multicellular life: (1) the presence of many early taxa with low membership and high rank is an artifact of naming; (2) cladistic analysis of Burgess arthropods negates the claim for greater early disparity; and (3) Whittington's argument is a retrospective fallacy based on assigning high rank to differentia only by virtue of their later capacity to define major branches. I show that all these arguments are either false or illogical, and that the claim for increased early disparity is justified: (1) Taxonomic rank is an artifact, but no one has ever based a claim for greater disparity on this false criterion. (2) Cladistics can only deal with branching order, whereas disparity is a phenetic issue. These two legitimate aspects of evolutionary “relationship” are logically distinct. The rooting of a cladogram only illustrates monophyletic ancestry (which no one doubts, as we are not creationists), and cannot measure disparity. (3) The active stabilization of the differentia ofBaupläne(for genetic and developmental reasons only dimly understood) provides a powerful rationale for weighting these characters in considerations of disparity; nothing had so stabilized in the Burgess fauna. If these differentia were steadily changing contingencies, rather than actively stabilized features with “deep” architectural status, then the retrospective argument would be justified. Although the three arguments are wrong, the claim for greater early disparity cannot be confidently established until we develop quantitative techniques for the characterization of morphospace and its differential filling through time. This is a dauntingly difficult problem, much harder than cladistic ordering, but not intractable.

scholarly journals Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses

2020 ◽  
Vol 94 (8) ◽  
Author(s):  
Eugene Christo-Foroux ◽  
Jean-Marie Alempic ◽  
Audrey Lartigue ◽  
Sebastien Santini ◽  
Karine Labadie ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Plant Diseases ◽  
Close Relative ◽  
Homologous Proteins ◽  
New Era ◽  
Environmental Virology ◽  
Double Stranded Dna ◽  
Giant Viruses ◽  
Incomplete Picture

ABSTRACT Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry. IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.

scholarly journals Isolation of A Novel Bacillus thuringiensis Phage Representing A New Phage Lineage and Characterization of Its Endolysin

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 611 ◽  
Author(s):  
Yihui Yuan ◽  
Qin Peng ◽  
Shuo Yang ◽  
Shaowen Zhang ◽  
Yajuan Fu ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Pathogenic Bacteria ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Host Bacterium ◽  
The Novel ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

Phages, the parasites of bacteria, are considered as a new kind of antimicrobial agent due to their ability to lyse pathogenic bacteria. Due to the increase of available phage isolates, the newly isolated phage showed increasing genomic similarities with previously isolated phages. In this study, the novel phage vB_BthS_BMBphi, infecting the Bacillus thuringiensis strain BMB171, is isolated and characterized together with its endolysin. This phage is the first tadpole-like phage infecting the Bacillus strains. Genomic analysis shows that the phage genome is dissimilar to all those of previously characterized phages, only exhibiting low similarities with partial regions of the B. thuringiensis prophages. Phylogenetic analysis revealed that the phage was distant from the other Bacillus phages in terms of evolution. The novel genome sequence, the distant evolutionary relationship, and the special virion morphology together suggest that the phage vB_BthS_BMBphi could be classified as a new phage lineage. The genome of the phage is found to contain a restriction modification system, which might endow the phage with immunity to the restriction modification system of the host bacterium. The function of the endolysin PlyBMB encoded by the phage vB_BthS_BMBphi was analyzed, and the endolysin could lyse all the tested Bacillus cereus group strains, suggesting that the endolysin might be used in controlling pathogenic B. cereus group strains. The findings of this study enrich the understanding of phage diversity and provide a resource for controlling the B. cereus group pathogenic bacteria.

Characterization of a Chromosome-Specific Chimpanzee Alpha Satellite Subset: Evolutionary Relationship to Subsets on Human Chromosomes

Genomics ◽  
1996 ◽  
Vol 33 (2) ◽  
pp. 220-228 ◽  
Author(s):  
Peter E. Warburton ◽  
Thomas Haaf ◽  
John Gosden ◽  
Diane Lawson ◽  
Huntington F. Willard
Keyword(s):  
Evolutionary Relationship ◽  
Human Chromosomes ◽  
Alpha Satellite

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 Evolutionary relationship of the L- and M-class genome segments of bat-borne fusogenic orthoreoviruses in Malaysia and Australia

2011 ◽  
Vol 92 (12) ◽  
pp. 2930-2936 ◽  
Author(s):  
Kenny Voon ◽  
Kaw Bing Chua ◽  
Meng Yu ◽  
Gary Crameri ◽  
Jennifer A. Barr ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Evolutionary Relationship ◽  
Whole Genome ◽  
Gene Products ◽  
Genome Characterization ◽  
Genetic Lineages ◽  
Genetic Reassortment ◽  
Different Strains ◽  
Relationship Of

We previously described three new Malaysian orthoreoviruses designated Pulau virus, Melaka virus and Kampar virus. Melaka and Kampar viruses were shown to cause respiratory disease in humans. These viruses, together with Nelson Bay virus, isolated from Australian bats, are tentatively classified as different strains within the species Pteropine orthoreovirus (PRV), formerly known as Nelson Bay orthoreovirus, based on the small (S) genome segments. Here we report the sequences of the large (L) and medium (M) segments, thus completing the whole-genome characterization of the four PRVs. All L and M segments were highly conserved in size and sequence. Conserved functional motifs previously identified in other orthoreovirus gene products were also found in the deduced proteins encoded by the cognate segments of these viruses. Detailed sequence analysis identified two genetic lineages divided into the Australian and Malaysian PRVs, and potential genetic reassortment among the M and S segments of the three Malaysian viruses.

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