The Revised Classification of Eukaryotes

Adl, Sina M.; Simpson, Alastair G. B.; Lane, Christopher E.; Lukeš, Julius; Bass, David; Bowser, Samuel S.; Brown, Matthew W.; Burki, Fabien; Dunthorn, Micah; Hampl, Vladimı́r; Heiss, Aaron A.; Hoppenrath, Mona; Lara, Enrique; Gall, Line Le; Lynn, Denis H.; McManus, Hilary A.; Mitchell, Edward A. D.; Mozley‐Stanridge, Sharon E.; Parfrey, Laura Wegener; Pawłowski, Jan; Rueckert, Sonja; Shadwick, Laura; Schoch, Conrad L.; Smirnov, Alexey V.; Spiegel, Frederick W.

doi:10.1111/j.1550-7408.2012.00644.x

Cited by 1,438 publications

(1,204 citation statements)

References 203 publications

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“…The phylogenetic position of D. discoideum within the Amoebozoa supergroup, which branched off after plants (Archaeplastida) but before animals (Opisthokonta) [72], gives us glimpses into the evolution of the miRNA machinery. The miRNA pathway in D. discoideum share several features with plants.…”

Section: Resultsmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

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Section: Resultsmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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“…However, by stating that a protein is conserved, cell biologists and biochemists often simply mean that the protein is present in S. cerevisiae (fungi) and animals. Since the clade comprising animals and fungi only accounts for one fifth of the diversity of eukaryotes ( Adl et al , 2012), more work is necessary in order to support the claim made by Lahiri et al Thus, I was prompted to investigate the taxonomic distribution of the EMC in order to (1) determine if it really is a conserved protein complex and (2) if it could possibly represent the pan-eukaryotic ER-mitochondria tether.…”

Section: Introductionmentioning

confidence: 99%

The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?

Wideman

2015

F1000Res

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The recently discovered endoplasmic reticulum (ER) membrane protein complex (EMC) has been implicated in ER-associated degradation (ERAD), lipid transport and tethering between the ER and mitochondrial outer membranes, and assembly of multipass ER-membrane proteins. The EMC has been studied in both animals and fungi but its presence outside the Opisthokont clade (animals + fungi + related protists) has not been demonstrated. Here, using homology-searching algorithms, I show that the EMC is truly an ancient and conserved protein complex, present in every major eukaryotic lineage. Very few organisms have completely lost the EMC, and most, even over 2 billion years of eukaryote evolution, have retained a majority of the complex members. I identify Sop4 and YDR056C in Saccharomyces cerevisiae as Emc7 and Emc10, respectively, subunits previously thought to be specific to animals. This study demonstrates that the EMC was present in the last eukaryote common ancestor (LECA) and is an extremely important component of eukaryotic cells even though its primary function remains elusive.

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“…This additional information was compiled from the consulted literature as well as from our personal observations. Classification of the species at higher taxonomic levels fol-lowed Adl et al (2012). These authors proposed a hierarchical system of classification founded on robust phylogenetic relatedness that avoid the use of formal rank designations such as "class", "sub-class", "super-order", or "order".…”

Section: Database Constructionmentioning

confidence: 99%

“…Their sensitivity to slight changes in the environmental conditions has turned them into an increasingly (filose testate amoebae) (Adl et al 2012). Past estimations of their diversity reached about 2,000 species (Meisterfeld 2002a(Meisterfeld , 2002b.…”

Section: Introductionmentioning

confidence: 99%

Checklist, diversity and distribution of testate amoebae in Chile

Fernández

Lara

Mitchell

2015

European Journal of Protistology

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Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species−accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly, the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25 • S-47 • S). These findings are here thoroughly discussed in a biogeographical and evolutionary context.

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The Revised Classification of Eukaryotes

Cited by 1,438 publications

References 203 publications

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?

Checklist, diversity and distribution of testate amoebae in Chile

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