The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in ...fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.
Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, ...Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates - Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.
The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution ...in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them.
We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms, we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes.
With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution.
Life was microbial for the majority of Earth’s history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) ...amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae.
•Arcellinida testate amoebae are comprised of seven major lineages•Reconstructed hypothetical ancestral states are congruent with Tonian fossils•Combined analysis of phylogenies and fossils suggest divergence as early as 730 mya
Arcellinid testate amoebae are some of the earliest eukaryotic microbes. Lahr et al. show that these amoebae have seven major deep phylogenetic lineages, probably diverged as early as 730 mya. Diversification of these microbes in the mid-Neoproterozoic was probably happening alongside the gradual oxygenation of oceans.
Discoveries of diverse microbial eukaryotes and their inclusion in comprehensive phylogenomic analyses have crucially re-shaped the eukaryotic tree of life in the 21st century.1 At the deepest level, ...eukaryotic diversity comprises 9–10 “supergroups.” One of these supergroups, the Metamonada, is particularly important to our understanding of the evolutionary dynamics of eukaryotic cells, including the remodeling of mitochondrial function. All metamonads thrive in low-oxygen environments and lack classical aerobic mitochondria, instead possessing mitochondrion-related organelles (MROs) with metabolisms that are adapted to low-oxygen conditions. These MROs lack an organellar genome, do not participate in the Krebs cycle and oxidative phosphorylation,2 and often synthesize ATP by substrate-level phosphorylation coupled to hydrogen production.3,4 The events that occurred during the transition from an oxygen-respiring mitochondrion to a functionally streamlined MRO early in metamonad evolution remain largely unknown. Here, we report transcriptomes of two recently described, enigmatic, anaerobic protists from the genus Anaeramoeba.5 Using phylogenomic analysis, we show that these species represent a divergent, phylum-level lineage in the tree of metamonads, emerging as a sister group of the Parabasalia and reordering the deep branching order of the metamonad tree. Metabolic reconstructions of the Anaeramoeba MROs reveal many “classical” mitochondrial features previously not seen in metamonads, including a disulfide relay import system, propionate production, and amino acid metabolism. Our findings suggest that the cenancestor of Metamonada likely had MROs with more classical mitochondrial features than previously anticipated and demonstrate how discoveries of novel lineages of high taxonomic rank continue to transform our understanding of early eukaryote evolution.
•Deep transcriptomic sequencing of two new anaerobic metamonads•The Anaeramoebae represents a new principal lineage of Metamonada•Anaeramoebae are free-living relatives of the parasitic parabasalids•Retention of mitochondrial features in mitochondrion-related organelles
Stairs et al. report a new phylum-level lineage of eukaryotes named the Anaeramoebae. These free-living anaerobes represent a new branch on the tree of life that is sister to the parasitic parabasalids, including Trichomonas vaginalis. The Anaeramoebae have complex mitochondrial proteomes with features not found in their closest relatives.
Deep-seated gravitational slope deformations (DSGSDs) played an important role during the Quaternary evolution of mountain ridges formed by anisotropic flysch rocks of the Outer Western Carpathians ...(OWC). Four DSGSD-affected ridges in the highest part of the Czech sector of the OWC have been subjected to multidisciplinary investigation involving mapping, structural and kinematic analysis, geoelectrical imaging, trenching and dating. All the studied DSGSDs are strongly predisposed by regional structural fabric given by the intersection of bedding planes, joint sets and faults. Performed research suggests high diversity of mechanisms leading to the origin of individual DSGSDs. The area of a single DSGSD can be affected by various types of movements such as sackung, lateral spreading, toppling or incipient sliding. Electrical imaging and trenching revealed that besides these mechanisms, anisotropic flysch massifs formed by thick-bedded sandstones are strongly exposed to subsurface opening of air-filled voids related to widened crevices. Such a process is driven by deep-seated creep and translational sliding of sandstone beds upon plastic claystones whose strength has been reduced to residual values of the angle of internal friction. Performed radiocarbon and OSL dating revealed that some of the studied DSGSDs originated in the Holocene period, particularly in the Atlantic and Subboreal chronozones.
The Czech part of the Outer Western Carpathians (COWC) formed by flysch rocks is among the most landslide-prone areas in Europe. Recent LiDAR-based inventory mapping reveals that the area of the COWC ...encompasses more than 13,500 landslides, with some geological domains exhibiting > 20% of the surface area covered by landslides. Although mass movements represent crucial geomorphic agents in the COWC, their timing and especially lifespan remain elusive. In this study, we focused on rockslides affecting the flanks of the flysch anticline developed within Paleogene sandstones. The area (“Hradisko” ridge) is well known as the most extensive rock city in the COWC. Structural-geological investigation, kinematic analysis and the application of near-surface geophysics (ERT, GPR and seismic refraction) suggest that rockslides accompanied by toppling and lateral spreads are predisposed by the architecture of bedding planes, joints and inherited faults cross-cutting the anticlinal ridge. Based on
10
Be exposure dating of five scarps and rockslide boulders (a total of 25 cosmogenic-dated samples), we were able to reconstruct the long-term history of rock slope failures. Although the obtained ages of headscarp exposures reveal consistent patterns suggesting major mass movement phases at ~ 18 ka and ~ 12 ka, the interpretation of boulder exposure ages is ambiguous. The study area has not been affected by catastrophic slope failure in historic times, but dendrogeomorphic analysis reveals surprisingly strong tree ring signals of mass movements within the last 150 years. These findings suggest that progressive failure is developing within some parts of the rockslide and/or slope portions above the major scarp. We conclude the following: (1) some rockslide spots within the COWC might express a very long history, encompassing the full Late Glacial–Holocene Period; (2) major mass movement activity in the study site temporally coincided with the major climatic changes; (3) rockslides with a very long history still represent potential hazards, although evidence of their active movement is not detected by standard geomorphic mapping techniques and (4) dating of the scarps should be preferred as even a higher number of boulders might be unreliable.
Abstract
The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and ...the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest that they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and nonredundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.
The protist cultural renaissance del Campo, Javier; Carlos-Oliveira, Maria; Čepička, Ivan ...
Trends in microbiology (Regular ed.),
02/2024, Letnik:
32, Številka:
2
Journal Article
Recenzirano
Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, ...concluding with actions required for a successful return of the golden age of protist culturing.
Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.
Landslides are an important natural phenomenon of the flysch Outer Western Carpathians that diversify the local topography and provide valuable microrefugia in the geomorphologically uniform region. ...For the first time, we reconstructed the continuous history of Carpathian landslide wetland – the Kotelnice mire, which initiated at the Pleistocene-Holocene transition, using joint analysis of abiotic proxies, pollen, plant macrofossils and testate amoebae (TA). We utilised modern training datasets of plants and TA to define ecological requirements of species and to determine indicators of either bog or fen habitats. We further compared pollen representation of selected woody species between two landslide-related wetlands and two spring fens, not related to landslides within the study region. The unique feature of the Kotelnice mire is the development of a nearly ombrotrophic bog at ∼2500 cal BP that was after ∼1500 years reversed to a poor fen by intense deforestation and pastoralism. Pollen analysis and its intra-regional comparison demonstrate a dual refugial role of landslides in the Carpathians. In the Early Holocene and perhaps even in the Late Glacial, landslides provided refugia for warmth- and moisture-demanding species (e.g. lime, elm, hazel, beech, maple). On the contrary, they provided shelter for cold-demanding boreal species (e.g. spruce, Eriophorum vaginatum, Sphagnum medium/divinum) in the Middle and Late Holocene. Because the analogous refugial role of landslides at both the recent and the Quaternary time scales has been reported from the flysch-like and volcanite bedrocks across the Northern Hemisphere, landslides deserve more attention in searching for regionally or even globally crucial refugia.
•Landslide wetland deposits witness landscape changes since the Late Glacial.•Landslides may support heterogeneity and refugial survivals in the Carpathians.•At the Holocene onset, mesophilic trees were more common in landslide areas.•In the studied landslide wetland, a nearly raised bog developed at ∼2500 cal BP.•Deforestation and pastoralism reversed the bog back to a poor fen ∼400 years ago.
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