Going Forward and Back: The Complex Evolutionary History of the GPx

There is large diversity among glutathione peroxidase (GPx) enzymes regarding their function, structure, presence of the highly reactive selenocysteine (SeCys) residue, substrate usage, and reducing agent preference. Moreover, most vertebrate GPxs are very distinct from non-animal GPxs, and it is still unclear if they came from a common GPx ancestor. In this study, we aimed to unveil how GPx evolved throughout different phyla. Based on our phylogenetic trees and sequence analyses, we propose that all GPx encoding genes share a monomeric common ancestor and that the SeCys amino acid was incorporated early in the evolution of the metazoan kingdom. In addition, classical GPx and the cysteine-exclusive GPx07 have been present since non-bilaterian animals, but they seem to have been lost throughout evolution in different phyla. Therefore, the birth-and-death of GPx family members (like in other oxidoreductase families) seems to be an ongoing process, occurring independently across different kingdoms and phyla.

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The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases

10.1101/2020.01.27.920793 ◽

2020 ◽

Cited By ~ 3

Author(s):

Leny M. van Wijk ◽

Berend Snel

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Evolutionary Dynamics ◽

Common Ancestor ◽

Cell Signalling ◽

Eukaryotic Cell ◽

Functional Information ◽

Last Eukaryotic Common Ancestor ◽

History Of ◽

Human Kinome

AbstractEukaryotic Protein Kinases (ePKs) are essential for eukaryotic cell signalling. Several phylogenetic trees of the ePK repertoire of single eukaryotes have been published, including the human kinome tree. However, a eukaryote-wide kinome tree was missing due to the large number of kinases in eukaryotes. Using a pipeline that overcomes this problem, we present here the first eukaryotic kinome tree. The tree reveals that the Last Eukaryotic Common Ancestor (LECA) possessed at least 92 ePKs, much more than previously thought. The retention of these LECA ePKs in present-day species is highly variable. Fourteen human kinases with unresolved placement in the human kinome tree were found to originate from three known ePK superfamilies. Further analysis of ePK superfamilies shows that they exhibit markedly diverse evolutionary dynamics between the LECA and present-day eukaryotes. The eukaryotic kinome tree thus unveils the evolutionary history of ePKs, but the tree also enables the transfer of functional information between related kinases.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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Rhizobial plasmids — replication, structure and biological role

Open Life Sciences ◽

10.2478/s11535-012-0058-8 ◽

2012 ◽

Vol 7 (4) ◽

pp. 571-586 ◽

Cited By ~ 8

Author(s):

Andrzej Mazur ◽

Piotr Koper

Keyword(s):

Genome Organization ◽

Soil Bacteria ◽

Evolutionary History ◽

Bacterial Genome ◽

Biological Role ◽

Genome Architecture ◽

Genomic Knowledge ◽

History Of ◽

Cryptic Plasmids ◽

Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

10.1101/766360 ◽

2019 ◽

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis Enrique Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Common Ancestor ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Common Ancestry ◽

Demethylation Pathway ◽

History Of ◽

New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life

American Journal of Botany ◽

10.1002/ajb2.1066 ◽

2018 ◽

Vol 105 (3) ◽

pp. 315-329 ◽

Cited By ~ 7

Author(s):

Hilary A. McManus ◽

Karolina Fučíková ◽

Paul O. Lewis ◽

Louise A. Lewis ◽

Kenneth G. Karol

Keyword(s):

Evolutionary History ◽

Tree Of Life ◽

Green Algal ◽

Plastid Genomes ◽

History Of ◽

Complex Evolutionary History

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A total evidence approach using palynological characters to infer the complex evolutionary history of the Asian Impatiens (Balsaminaceae)

Taxon ◽

10.1002/tax.612007 ◽

2012 ◽

Vol 61 (2) ◽

pp. 355-367 ◽

Cited By ~ 10

Author(s):

Steven B. Janssens ◽

Yi Song Wilson ◽

Yong-Ming Yuan ◽

Anne Nagels ◽

Erik F. Smets ◽

...

Keyword(s):

Evolutionary History ◽

Total Evidence ◽

History Of ◽

Complex Evolutionary History

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INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720006001709 ◽

2006 ◽

Vol 04 (01) ◽

pp. 59-74 ◽

Cited By ~ 20

Author(s):

YING-JUN HE ◽

TRINH N. D. HUYNH ◽

JESPER JANSSON ◽

WING-KIN SUNG

Keyword(s):

Approximation Algorithms ◽

Phylogenetic Tree ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Phylogenetic Network ◽

Evolutionary Relationships ◽

Large Set ◽

Tree Network ◽

History Of ◽

Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

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