Evolution of Archamoebae: Morphological and Molecular Evidence for Pelobionts Including Rhizomastix, Entamoeba, Iodamoeba, and Endolimax

Ptáčková, Eliška; Kostygov, Alexei Y.; Chistyakova, L. V.; Falteisek, Lukáš; Frolov, Andrei N.; Patterson, David J.; Walker, Gordon; Čepička, Ivan

doi:10.1016/j.protis.2012.11.005

Cited by 45 publications

(64 citation statements)

References 81 publications

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“…At the same time, in Korotnevella spp. (Zlatogursky et al 2016) and some of the archamoebids (in particular, Mastigamoeba abducta and Rhizomastix libera; Ptáčková et al 2013) the pattern of variability seems to be similar to our findings in Ripella. For example, in the studied species of Korotnevella the SSU rRNA gene variability within a clonal strain reached 9.4%, and besides random substitutions several repeated nucleotide motifs were detected in the helices 43 and 45/e1 (regions V7 and V8).…”

Section: Unusual Pattern Of Ssu Rrna Gene Variability In Ripellasupporting

confidence: 88%

“…Further, Nassonova et al (2010) demonstrated sequence divergence at the level of up to 3.2% in the SSU rRNA gene and up to 7.5% in the ITS1-5.8S-ITS2 locus in Vannella spp. Similar variability in the SSU rRNA gene was shown in Himatismenida (Geisen et al 2014;, Arcellinida (Kudryavtsev et al 2009), Pellitida , some of the Archamoebae (Ptáčková et al 2013) and some of the Dactylopodida (Kudryavtsev and Pawlowski 2015;Zlatogursky et al 2016). In most of the above-cited papers the detected variability of the ribosomal genes within the genome appears to be random.…”

Section: Unusual Pattern Of Ssu Rrna Gene Variability In Ripellasupporting

confidence: 57%

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Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Kudryavtsev

Гладких

2017

European Journal of Protistology

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Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.

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Section: Unusual Pattern Of Ssu Rrna Gene Variability In Ripellasupporting

confidence: 88%

Section: Unusual Pattern Of Ssu Rrna Gene Variability In Ripellasupporting

confidence: 57%

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Kudryavtsev

Гладких

2017

European Journal of Protistology

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“…Recent studies have identified other anaerobic/microaerophilic protists that are members of the archamoebae, including Iodamoeba and Rhizomastix, that lack typical cristate mitochondria [91,92], but have MRO-like organelles in electron micrographs.…”

Section: Amoebozoa (A) Archamoebaementioning

confidence: 99%

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

Stairs

Leger

Roger

2015

Phil. Trans. R. Soc. B

135

172

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes ( protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.

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“…Subsequently, remnants of mitochondria were reported from several of its species (e.g. Clark and Roger, 1995;Tovar et al, 1999;Walker et al, 2001;Gill et al, 2007;Ptáčková et al, 2013, Zadrobílková et al 2015a).…”

Section: Introductionmentioning

confidence: 99%

First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group

Pánek

Zadrobílková

Walker

et al. 2016

Molecular Phylogenetics and Evolution

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Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.

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Evolution of Archamoebae: Morphological and Molecular Evidence for Pelobionts Including Rhizomastix, Entamoeba, Iodamoeba, and Endolimax

Cited by 45 publications

References 81 publications

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group

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