scholarly journals Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida

Antioxidants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 597
Author(s):  
Fernanda Lazzarotto ◽  
Paloma Koprovski Menguer ◽  
Luiz-Eduardo Del-Bem ◽  
Marcel Zámocký ◽  
Márcia Margis-Pinheiro
Keyword(s):  
Phylogenetic Analysis ◽  
Green Algae ◽  
Ascorbate Peroxidase ◽  
Peroxidase Activity ◽  
The Other ◽  
Hybrid Proteins ◽  
Catalytic Sites ◽  
Molecular Phylogenetic ◽  
Binding Residues ◽  
L Proteins

Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization.

scholarly journals Ascorbate peroxidase neofunctionalization at the origin of APx-R and APx-L: evidences from basal Archaeplastida

2020 ◽  
Author(s):  
Fernanda Lazzarotto ◽  
Paloma Koprovski Menguer ◽  
Luiz-Eduardo Del-Bem ◽  
Márcia Margis-Pinheiro
Keyword(s):  
Ascorbate Peroxidase ◽  
Peroxidase Activity ◽  
Binding Sites ◽  
The Other ◽  
Class I ◽  
Hybrid Proteins ◽  
Catalytic Sites ◽  
Molecular Phylogenetic ◽  
Binding Residues ◽  
L Proteins

AbstractAscorbate peroxidases (APx) are class I members of the non-animal peroxidases superfamily, a large group of evolutionarily related enzymes. Through mining in public databases, our group has previously identified two unusual subsets of APx homologs, disclosing the existence of two uncharacterized families of class I peroxidases, which were named ascorbate peroxidase-related (APx-R) and ascorbate peroxidase-like (APx-L). As APx, APx-R proteins possess all catalytic residues required for peroxidase activity. Nevertheless, these proteins do not contain residues known to be critical for ascorbate binding, implying that members of this family must use other substrates while reducing hydrogen peroxide. On the other hand, APx-L proteins not only lack ascorbate-binding residues, as do not contain any residue known to be essential for peroxidase activity, in contrast with every other member of the non-animal peroxidase superfamily, which is composed by over 10,000 proteins distributed among bacteria, archaea, fungi, algae, and plants. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, we now show the existence of hybrid proteins, which combine features of these three families. Analysis performed on public databases show that the prevalence of these proteins varies among distinct groups of organisms, accounting for up to 33% of total APx homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APx-R and APx-L, through a process characterized by the progressive deterioration of ascorbate-binding sites and catalytic sites towards neofunctionalization.

Molecular phylogeny of the genus Rhabdosciadium (Apiaceae) with description of a new species R. anatolyi from Hakkâri province, eastern Turkey

Phytotaxa ◽  
2017 ◽  
Vol 331 (2) ◽  
pp. 253
Author(s):  
DMITRY LYSKOV ◽  
EUGENE KLJUYKOV ◽  
EBRU DOĞAN GÜNER ◽  
TAHIR SAMIGULLIN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Phylogeny ◽  
Taxonomic Status ◽  
The Other ◽  
Monophyletic Group ◽  
Geographical Range ◽  
Eastern Turkey ◽  
Molecular Phylogenetic ◽  
A New Species

Six species of the genus Rhabdosciadium (Apiaceae) were studied by molecular phylogenetic analysis. The taxonomic status of each of them has been confirmed, the genus Rhabdosciadium turns out as a well-supported monophyletic group closely related to the genera Aegopodium, Caropodium, Carum, Falcaria, Fuernrohria, Gongylosciadium, Grammosciadium s.s., Hladnikia, Olymposciadium, etc. Rhabdosciadium anatolyi sp. nov. is described and illustrated as a new species from Hakkâri province, eastern Turkey. It differs from the other taxa of the genus, in addition to its unique geographical range, in the large terminal leaf lobes with regularly serrated margin, mainly ternate primary basal segments of leaves, and long internodes.

scholarly journals New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

2021 ◽  
Vol 12 ◽  
Author(s):  
Mingzhen Ma ◽  
Yuqing Li ◽  
Qingxiang Yuan ◽  
Xuetong Zhao ◽  
Khaled A. S. Al-Rasheid ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Freshwater Lake ◽  
The Other ◽  
Sufficient Evidence ◽  
Rdna Sequences ◽  
The Family ◽  
Molecular Phylogenetic

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

A new species of Tetrataenium (Tordyliinae, Apiaceae) from SW Yunnan, China, based on morphological and molecular data

Phytotaxa ◽  
2021 ◽  
Vol 491 (1) ◽  
pp. 85-91
Author(s):  
ZE-HUAN WANG ◽  
YI WANG ◽  
BAO-LIN LIU ◽  
CHAO-HE WANG ◽  
XIAN-GUO FU
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Data ◽  
Sensu Stricto ◽  
The Other ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Morphological And Molecular Data ◽  
A New Species

Tetrataenium mianguaqi, a traditionally used medicinal herb in Cangyuan County, SW Yunnan, China, is described as a species new to science and illustrated. Molecular phylogenetic analysis based on nuclear ITS well supports its belonging to Tetrataenium sensu stricto. The new species can be easily distinguished by its unique peltate, palmatilobate basal and lower leaves from the other five Chinese Tetrataenium species.

scholarly journals Phylogenetic relationships of 'Polyalthia' in Fiji

PhytoKeys ◽  
2020 ◽  
Vol 165 ◽  
pp. 99-113
Author(s):  
Bine Xue ◽  
Yanwen Chen ◽  
Richard M. K. Saunders
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
The Other ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Herbarium Specimens ◽  
Molecular Phylogenetic ◽  
Taxonomic Changes

The genus Polyalthia (Annonaceae) has undergone dramatic taxonomic changes in recent years. Nine Polyalthia species have historically been recognized in Fiji, all of which have subsequently been transferred to three different genera, viz. Goniothalamus, Huberantha and Meiogyne. The transfer of six of these species has received strong molecular phylogenetic support, although the other three species, Polyalthia amoena, P. capillata and P. loriformis [all transferred to Huberantha], have never previously been sampled in a phylogenetic study. We address this shortfall by sampling available herbarium specimens of all three species and integrating the data in a molecular phylogenetic analysis. The resultant phylogeny provides strong support for the transfer of these species to Huberantha. The taxonomic realignment of all nine Fijian species formerly classified in Polyalthia is also clearly demonstrated and supported by the resultant phylogeny. The updated taxonomic treatments of the nine species, a key to the three genera and a key to the Fijian Huberantha species are provided.

Phylogenetic analysis using rDNA reveals polyphyly of Oplophoridae (Decapoda:Caridea)

2010 ◽  
Vol 24 (2) ◽  
pp. 172 ◽  
Author(s):  
Tin-Yam Chan ◽  
Ho Chee Lei ◽  
Chi Pang Li ◽  
Ka Hou Chu
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Morphological Characters ◽  
The Other ◽  
Rrna Genes ◽  
Deep Channel ◽  
The Family ◽  
Molecular Phylogenetic ◽  
18S Rrna Genes ◽  
Molar Process

Molecular phylogenetic analysis on nine of the ten genera in the caridean family Oplophoridae Dana, 1852, as well as 14 other caridean families using mitochondrial 16S and nuclear 18S rRNA genes, does not support the monophyletic status of Oplophoridae. Two disparate groups of oplophorids are revealed, with different morphological characters and ecology. It is proposed that the family Oplophoridae is restricted to the three genera Oplophorus, Systellaspis and Janicella. These three genera tend to be distributed in shallower water than the other oplophorid genera, and can also be distinguished from them by certain morphological characters. They have a thicker integument, superficial cuticular photophores and larger eyes, and the molar process of their mandibles is greatly reduced or bears a deep channel. The family Acanthephyridae Bate, 1888 is resurrected for the other seven genera, which are generally distributed in deeper water and are characterised by red soft integument, no cuticular photophores, smaller eyes and well-developed molar process of the mandibles without a deep channel. The relationships between these two families and other caridean families could not be clearly resolved in this study.

scholarly journals Oreocharis jasminina (Gesneriaceae), a new species from mountain tops of Hainan Island, South China

PhytoKeys ◽  
2020 ◽  
Vol 157 ◽  
pp. 121-135
Author(s):  
Shao-Jun Ling ◽  
Shu-Ping Guan ◽  
Fang Wen ◽  
Yu-Min Shui ◽  
Ming-Xun Ren
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
South China ◽  
Hainan Island ◽  
The Other ◽  
Molecular Phylogenetic Analysis ◽  
Floral Tube ◽  
Floral Isolation ◽  
Molecular Phylogenetic ◽  
A New Species

A new species of Gesneriaceae, Oreocharis jasminina S.J.Ling, F.Wen & M.X. Ren from Hainan Island, south China, is highlighted and described. The new species is distinguished by its actinomorphic corolla, narrow floral tube and ovate anthers hidden in the floral tube. The new species also showed clear geographic and altitudinal isolation from the three currently-recognised Oreocharis species on the Island. Molecular phylogenetic analysis, based on nuclear ITS1/2 and plastid trnL-trnF sequences, supported the delimitation of the new species, which forms a single lineage with all the other Oreocharis species from Hainan Island. The roles of geographic and floral isolation in the evolution of the new species and its affinities are discussed.

An ESR study of the peroxidase reaction catalyzed by human methaemoglobin and methaemoglobin-haptoglobin complex

1991 ◽  
Vol 56 (4) ◽  
pp. 923-932
Author(s):  
Jana Stejskalová ◽  
Pavel Stopka ◽  
Zdeněk Pavlíček
Keyword(s):  
Hydrogen Peroxide ◽  
Ascorbic Acid ◽  
Amino Acid ◽  
Peroxidase Activity ◽  
Amino Acid Analysis ◽  
Superoxide Radical ◽  
Esr Spectra ◽  
The Other ◽  
Delocalized Electron

The ESR spectra of peroxidase systems of methaemoglobin-ascorbic acid-hydrogen peroxide and methaemoglobin-haptoglobin complex-ascorbic acid-hydrogen peroxide have been measured in the acetate buffer of pH 4.5. For the system with methaemoglobin an asymmetrical signal with g ~ 2 has been observed which is interpreted as the perpendicular region of anisotropic spectrum of superoxide radical. On the other hand, for the system with methaemoglobin-haptoglobin complex the observed signal with g ~ 2 is symmetrical and is interpreted as a signal of delocalized electron. After realization of three repeatedly induced peroxidase processes the ESR signal of the perpendicular part of anisotropic spectrum of superoxide radical is distinctly diminished, whereas the signal of delocalized electron remains practically unchanged. An amino acid analysis of methaemoglobin along with results of the ESR measurements make it possible to derive a hypothesis about the role of haptoglobin in increasing of the peroxidase activity of methaemoglobin.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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