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Amoebozoa are a type of protist that is characterized by the presence of pseudopodia which they use for locomotion and feeding.
- Describe characteristics of Amoebozoa
- Amoebozoa (amoebas) can live in either marine and fresh water or in soil.
- Amoebozoa are characterized by the presence of pseudopodia, which are extensions that can be either tube-like or flat lobes and are used for locomotion and feeding.
- Amooebozoa can be further divided into subclassifications that include slime molds; these can be found as both plasmodial and cellular types.
- Plasmodial slime molds are characterized by the presence of large, multinucleate cells that have the ability to glide along the surface and engulf food particles as they move.
- Cellular molds are characterized by the presence of independent amoeboid cells during times of nutrient abundancy and the development of a cellular mass, called a slug, during times of nutrient depletion.
- Archamoebae, Flabellinea, and Tubulinea are also groups of Amoebozoa; their defining characteristics include: Archamoebae lack mitochondria; Flabellinea flatten during locomotion and lack a shell and flagella; Tubulinea have a rough cylindrical form during locomotion with cylindrical pseudopodia.
- rhizaria: a species-rich supergroup of mostly unicellular eukaryotes that for the most part are amoeboids with filose, reticulose, or microtubule-supported pseudopods
- plasmodium: a mass of cytoplasm, containing many nuclei, created by the aggregation of amoeboid cells of slime molds during their vegetative phase
- sporangia: an enclosure in which spores are formed (also called a fruiting body)
Protists are eukaryotic organisms that are classified as unicellular, colonial, or multicellular organisms that do not have specialized tissues. This identifying property sets protists apart from other organisms within the Eukarya domain. The amoebozoans are classified as protists with pseudopodia which are used in locomotion and feeding. Amoebozoans live in marine environments, fresh water, or in soil. In addition to the defining pseudopodia, they also lack a shell and do not have a fixed body. The pseudopodia which are characteristically exhibited include extensions which can be tube-like or flat lobes, rather than the hair-like pseudopodia of rhizarian amoeba. Rhizarian amoeba are amoeboids with filose, reticulose, or microtubule-supported pseudopods and include the groups: Cercozoa, Foraminifera, and Radiolaria and are classified as bikonts. The Amoebozoa include several groups of unicellular amoeba-like organisms that are free-living or parasites that are classified as unikonts. The best known and most well-studied member of this group is the slime mold. Additional members include the Archamoebae, Tubulinea, and Flabellinea.
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore -generating fruiting bodies, similar to fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells that move along surfaces like an amorphous blob of slime during their feeding stage. Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia. These spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The cellular slime molds function as independent amoeboid cells when nutrients are abundant. When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Archamoebae, Flabellinea, and Tubulinea
The Archamoebae are a group of Amoebozoa distinguished by the absence of mitochondria. They include genera that are internal parasites or commensals of animals (Entamoeba and Endolimax). A few species are human pathogens, causing diseases such as amoebic dysentery. The other genera of archamoebae live in freshwater habitats and are unusual among amoebae in possessing flagella. Most have a single nucleus and flagellum, but the giant amoeba, Pelomyxa, has many of each.
The Tubulinea are a major grouping of Amoebozoa, including most of the larger and more familiar amoebae like Amoeba, Arcella, and Difflugia. During locomotion, most Tubulinea have a roughly cylindrical form or produce numerous cylindrical pseudopods. Each cylinder advances by a single central stream of cytoplasm, granular in appearance, and has no subpseudopodia. This distinguishes them from other amoeboid groups, although in some members this is not the normal type of locomotion.
23.3F: Amoebozoa and Opisthokonta - Biology
Figure 1. Sphaeroeca, a colony of choanoflagellates (aproximately 230 individuals)
The opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and, in fact, all animals.
Choanoflagellates include unicellular and colonial forms, and number about 244 described species. These organisms exhibit a single, apical flagellum that is surrounded by a contractile collar composed of microvilli. The collar uses a similar mechanism to sponges to filter out bacteria for ingestion by the protist. The morphology of choanoflagellates was recognized early on as resembling the collar cells of sponges, and suggesting a possible relationship to animals.
The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology. Some phylogenetic trees still group animals and fungi into the Opisthokonta supergroup though this is also considered a protist specific group in other phylogenies.
The eukaryotic membrane trafficking system is a network of interconnected organelles, each maintaining distinct protein and lipid compositions. Bidirectional membrane trafficking in all eukaryotic cells can be thought of as originating either at the endoplasmic reticulum (ER), for anterograde or secretory traffic, or at the plasma membrane for retrograde or endocytic traffic (Bonifacino, 2014). Whereas some other eukaryotic organelles are derived from ancient symbioses (e.g., mitochondria and plastids, with α-proteobacteria and cyanobacteria, respectively), the membrane trafficking system is believed to have arisen autogenously (Keeling and Koonin, 2014). How a complex network of organelles can arise from a cellular configuration with little to no subcompartmentalization is one of the largest remaining questions in evolutionary biology.
The organelle paralogy hypothesis (OPH) proposes an evolutionary mechanism to explain the complexity of membrane-trafficking organelles (Dacks and Field, 2007). The process of membrane trafficking is divided into two essential phases: vesicle formation, whereby cargo destined for transport are selected and packaged into membrane-bound vesicular carriers, and vesicle fusion, whereby the vesicles fuse and deliver their cargo to target organelles (Springer et al., 1999). Each of these processes depends on molecular components that are increasingly well understood, although far more complicated than originally envisioned. Although first described in animal and fungal model organisms, comparative genomic and phylogenetic analyses have demonstrated the conservation of much of the molecular machinery responsible for vesicle formation and fusion in diverse eukaryotes and by deduction in the last eukaryotic common ancestor (LECA) (Dacks and Field, 2018). The basis of the OPH is the observation that a limited number of paralogous protein families govern the major steps of membrane trafficking, with different paralogues from each family carrying out essentially the same functions at different steps along the route. The OPH postulates that gene duplication, followed by sequence divergence and coevolution of interacting members of different families to create preferential partnerships between organelle-specific paralogues, would have facilitated the emergence of novel organelles (Dacks and Field, 2007).
Regulatory GTPases control or modulate a wide array of cellular systems and are central to cellular responses to extracellular stimuli, maintenance of homeostasis, and communication between different parts of the eukaryotic cell (Cherfils and Zeghouf, 2013). A critical element of the vesicle formation process is the action of ADP-ribosylation factors (ARFs) and their regulators (Kahn, 2009 Donaldson and Jackson, 2011). ARFs are ∼21 kDa, monomeric GTPases that nucleate vesicle formation on organellar membranes (Kahn et al., 2006). Like all regulatory GTPases, ARFs cycle between active GTP-bound and inactive GDP-bound states. This cycling is mediated by two classes of regulatory proteins. ARF guanine nucleotide exchange factors (ARF GEFs) activate ARF signaling by increasing the rate of release of bound GDP from its target GTPase, resulting in a GEF-(apo) GTPase intermediate that dissociates on the binding of GTP (Shin and Nakayama, 2004 Zeghouf et al., 2005 Casanova, 2007). ARF GTPase-activating proteins (ARF GAPs) bind specifically to the activated (GTP-bound) form of ARFs, increase the rate of GTP hydrolysis, and thereby can terminate ARF signaling (Kahn et al., 2008 Spang et al., 2010 Vitali et al., 2017). GAPs and GEFs are important components of ARF signaling pathways as ARFs release GDP very slowly in the absence of a GEF and hydrolyze them either not at all or very slowly in the absence of a GAP. GEFs are the initiators of this essential signaling and as such play fundamental roles in an equally large fraction of all cell biology (Cherfils and Zeghouf, 2013). GEFs act on specific subsets or families of regulatory GTPases and themselves comprise several families and subfamilies. ARF GAPs also, somewhat paradoxically, typically serve as effectors as well as signal terminators (Zhang et al., 1998 East and Kahn, 2011). Thus, these modulators are essential components that provide temporal and spatial resolution to signaling by this essential family of regulatory GTPases.
In animals, there are six ARF paralogues (ARF1-6) that share a high degree (>65%) of primary sequence identity. The LECA has been reconstructed to have possessed only a single ARF (Li et al., 2004). Similarly, comparative genomic analyses sampling the breadth of eukaryotes allowed the discrimination of 11 subfamilies of ARF GAPs, of which six were present in the LECA, two were animal-specific, one was opisthokont-specific, and one was lost in opisthokonts (Schlacht et al., 2013). To gain a more complete understanding of the evolution of the ARF system, a complementary analysis of the ARF GEFs is needed.
ARF GEFs have been identified, and in fact are defined, by the presence of the Sec7 domain (Chardin et al., 1996 Cherfils et al., 1998). Note that, while we use the terms ARF GEF and Sec7 domain-containing proteins interchangeably herein, only a very few of the proteins analyzed have been shown to possess ARF GEF activity, and the specificities of even those for different GTPases are incompletely characterized. Given the size and complexity in domain organization among the ARF GEFs, it is quite likely that at least some have other activities and functions in cells, although this issue is not explored further here. In addition, the presence (or absence) of domains outside Sec7 have been shown to play critical roles in regulating the GEF activity, in recruitment of the protein to its site of action, and in binding to lipids and other proteins (Chantalat et al., 2004 Casanova, 2007 Malaby et al., 2013 Wright et al., 2014). There remains much unexplored diversity in domain organization and this comparative genomics analysis is the first step to uncovering novel ARF GEF function(s).
The Sec7 domain is ∼200 amino acid residues in length, encodes the nucleotide exchange activity, and is the target of the fungal toxin brefeldin A (BFA) (Peyroche et al., 1996). BFA is used extensively in the functional dissection of ARF pathways as it is membrane-permeant, rapidly acting, readily reversible, and appears to be a specific inhibitor of a subset of ARF GEFs that act at the Golgi (Fujiwara et al., 1988). The mechanism of BFA action involves its stabilization of an ARF-GDP-Sec7 domain complex and structural studies identified the key residues within the Sec7 domain that determine its sensitivity or resistance to BFA (Peyroche et al., 1999), a basis on which the six animal ARF GEFs have been classified.
The paradoxically named Golgi BFA-resistant factor 1 (GBF1) is in fact sensitive to BFA but was first cloned in a screen that overexpressed the protein and conferred BFA resistance to the cells (Claude et al., 1999). GBF1 has previously been shown to be pan-eukaryotic (Cox et al., 2004 Bui et al., 2009). GBF1 is involved in the ARF-dependent recruitment of COPI to the cis-Golgi and the ERGIC (ER-Golgi intermediate compartment) and is able to interact with both class I (ARF1-3) and class II (ARF4, 5) ARFs in mammalian cells (Zhao et al., 2006 Bouvet et al., 2013 Jackson, 2014). In Arabidopsis thaliana, the GBF1 homologue GNOM localizes to endosomes (Geldner et al., 2003). Rather than this representing differences in GBF1 functions between organisms, it is likely that GBF1 (and perhaps all ARF GEFs) localizes to multiple sites in cells and that the fractional occupancy at any one site differs between organisms or cell types. The other subfamily of BFA-sensitive ARF GEFs is the aptly named BFA-inhibited GEFs (BIGs). BIGs have also been found in diverse eukaryotic taxa (Cox et al., 2004 Bui et al., 2009 Mouratou et al., 2005) and are involved in regulating ARF-dependent trafficking at the trans-Golgi network (TGN) and at recycling endosomes (Shinotsuka et al., 2002a,b). GBF1 and BIG proteins in animals possess characteristic domain organizations (Figure 1). Dimerization and cyclophilin binding (DCB) and homology upstream of Sec7 (HUS) domains are found upstream of the Sec7 domain, and homology downstream of Sec7 (HDS) 1, 2, and 3 are downstream of the Sec7 domain in both proteins, while an additional HDS (HDS4) is present in BIGs (Mouratou et al., 2005).
FIGURE 1: Ancestral configuration of domains in the ARF GEF subfamilies. Conserved domains present in and that help define each ARF GEF subfamily are shown. These represent the configurations likely found in the ancestral sequence of each subfamily. The domain organization of ARF GEF proteins found in the human proteins is conserved across the entire distribution of each subfamily and represents the domains present in the earliest ancestor of each subfamily. Dotted representation of the cytohesin PH domain indicates frequent independent loss of this domain. Non-opisthokonta ARF GEFs, TBS and ARCC, are also shown, based on their consistent distribution in multiple amoebozoan and SAR lineages. Ank, Ankyrin repeat DCB, dimerization and cyclophilin-binding domain F-box, F-box domain HDS1, homology downstream of Sec7 1 HDS2, homology downstream of Sec7 2 HDS3, homology downstream of Sec7 3 HDS4, homology downstream of Sec7 4 HUS, homology upstream of Sec7 IQ, IQ motif PH, pleckstrin homology domain Sec7, Sec7/ARF GEF catalytic domain TBC, Tre-2/Bub2/Cdc16 Rab GTPase domain. Linear depictions of each subfamily and domains are not drawn to scale, with approximate lengths indicated on the right. The number of Ank repeats varies, as indicated.
The BFA-resistant subfamilies of GEFs are the cytohesins, the BFA-resistant ARF GEFs (BRAGs, also known as IQSEC7 [IQ and Sec7 domain-containing]), exchange factor for ARF6 (EFA6), and F-box only protein 8 (FBX8). Some cytohesins have previously been named ARF guanine nucleotide site opener (Chardin et al., 1996) or general receptors for phosphoinositides 1 herein, we exclusively use the term cytohesin. Because the BRAG terminology is more prominent in the literature than is IQSEC7, we will occasionally use both (BRAG/IQSEC7) for clarity. Similarly, we prefer the EFA6 nomenclature to that of PSDs (PH and Sec7 Domain), as it is far more common in the ARF GEF field, and the acronym PSD is also used for the unrelated protein phosphatidylserine decarboxylase. Cytohesins localize primarily to the cell periphery, where they act as GEFs to activate several ARFs, most notably perhaps ARF6, but also others by recruitment of the ARFs to the plasma membrane via their PH domains (Macia et al., 2001 Cohen et al., 2007). At the plasma membrane they are involved in the docking and fusion of secretory granules, the endocytosis of G-protein coupled receptors, and have important roles in integrin-mediated cell adhesion and movement (Claing et al., 2000 Geiger et al., 2000 Liu et al., 2006). Cytohesins and IQSEC7s have each been identified in metazoa with the latter only found there (Cox et al., 2004). IQSEC7s localize to the plasma membrane where they regulate the endocytosis of specific cargo and interact with ARF6 (e.g., β-integrins Someya et al., 2001 Dunphy et al., 2006). EFA6 proteins are also localized to the plasma membrane and interact with both ARF1 and ARF6, serving to coordinate endocytosis, cytoskeletal dynamics, and maintenance of cellular junctions (Frank et al., 1998 Franco et al., 1999 Macia et al., 2001 Klein et al., 2008 Padovani et al., 2014). Cytohesins, EFA6, and IQSEC7s share the domain architecture of a Sec7 domain followed by a C-terminal PH domain, with IQSEC7s also possessing an N-terminal characteristic IQ domain (Figure 1). FBX8 is probably the least understood ARF GEF. It functions as part of a multisubunit ubiquitin-ligase complex, resulting in the suppression of ARF6 activity through its ubiquitination and subsequent degradation (Kipreos and Pagano, 2000 Cox et al., 2004 Yano et al., 2008). It is also unique in possessing an F-box domain N-terminal to the Sec7 domain, but no additional C-terminal domains (Figure 1).
A phylogenetic analysis of ARF GEFs was published previously (Cox et al., 2004), although at that time far fewer genomes had been sequenced and thus those analyses were performed on a far smaller collection of proteins from fewer species. Here, we have taken advantage of the large number of sequenced eukaryotic genomes to carry out detailed comparative genomic and phylogenetic analyses of Sec7 domain-containing proteins.
Zajednička karakteristika opistokonta je su bičaste ćelije, poput spermatozoida većine životinja i spore hitridnih gljiva, sa samo jednim "opisto" (stražnjim) bičem. Upravo ova karakteristika grupi daje ime. Suprotno tome, ćelije flagelata u drugim eukariotskim grupama pokreću jedan ili više prednjih flagela. Međutim, u nekim skupinama opisthokonta, uključujući većinu gljiva, ćelije su se potpuno izgubile. 
Karakteristike opistokonta uključuju opća svojstva kao što su
- sinteza vanćelijskog hitina u egzoskeletu, zidu cisti / spora ili ćelijskom zidu vlaknastog tijela i hifa
- vančelijska digestiju supstrata sa osmotrofnom apsorpcijom hranljivih sastojaka i
- drugi ćelijski biosintetski i metabolički put.
Rodovi u osnovi svakog kladusa su ameboidni i fagotrofni. 
Bliske odnose životinja i gljiva sugerirao je Thomas Cavalier-Smith, 1987.,  koji je koristio neformalno ime Opisthokonta (formalni naziv je 1956. koristio za Chytridiomycota od Copelanda), a podržale su ga i kasnije genetičke studije. 
Rane filogenije su postavile gljive u blizini biljaka i drugih grupa koje imaju mitohondrije sa ravnim kristama (grebenima), ali taj karakter varira. U novije vrijeme govorilo se da su holoza (životinje) i holomikota (gljive) međusobno mnogo bliže nego biljkama, jer opisthokonti imaju trostruko spajanje karbamoil-fosfat sintetaze, dihidroorotaze i aspartat karbamoiltransferaza kojih nema nije u biljkama, a biljke imaju fuziju timidilat sintaza i dihidrofolat reduktaza kojih nema u opistokontima. Životinje i gljive su također bliže amebama nego biljkama, a biljke su bliže supergrupi SAR protista nego životinjama ili gljivama. Životinje i gljive su heterotrofi, za razliku od biljaka, i dok su gljive sesilne poput biljaka, postoje i sesilne životinje.
Cavalier-Smith i Stechmann  tvrde da su se netrepljasti eukarioti kao što su opistokonte i Amoebozoa, skupno zvani Unikonta, odvojili od ostalih dvotrepljastih eukariota, nazvanih Bikonta, nedugo nakon što su se pojavili.
Opistokonte se dijele na Holomycota ili Nucletmycea (gljive i svi organizmi koji su bliže gljivama nego životinjama) i Holozoa (životinje i svi organizmi koji su bliže životinjama nego gljivama) još nije identificiran opistokont baziran na razdvajanje Holomycota / Holozoa. Taksonomiju opistokonti su u velikoj mjeri riješili Torriella et al.  Holomycota i Holozoa sastavljene su od slijedećih grupa:
- (bičari, gljive sa zoosporama)
- Fonticula (Filogenija novijih radova smatra ih dijrlovima Cristidiscoidea, sestrinske grupe gljiva)
- Hyaloraphidium (prethodno smatran da je zelena alga, sada se svrstava u gljive) (prethodno u Apicomplexia) (Novija filogenija smatra ih dijelom Cristidiscoidea, sestrinske grupe gljiva)
- Corallochytrium (bivše Heterokonta) (bičari, renije uključeni u Protozoa)
- ”some uniflagellate algal monads” [Protochlorinae? Pedilomonas, Chlorochytridion?]
- Kingdom Protoctista
- Phylum Opisthokonta
- Class Archimycetes
- Order 1. Monoblepharidalea
- Order 2. Chytridinea
Cavalier-Smith (1987) Edit
Cavalier-Smith, T. (1987). The origin of fungi and pseudofungi. In: Rayner, Alan D. M. (ed.). Evolutionary biology of Fungi. Cambridge: Cambridge Univ. Press. pp. 339–353. From Leadbeater (2015).
Hausmann et al. (2003) Edit
From Hausmann, K., N. Hulsmann, R. Radek. Protistology. Schweizerbart'sche Verlagsbuchshandlung, Stuttgart, 2003.
Empire Eukaryota Chatton, 1925 (= Eukarya)
- Phylum Opisthokonta Cavalier-Smith & Chao, 1995
- Subphylum Fungi Nees,1817
- Infraphylum Chytridiomycota de Вагу, 1863
- Infraphylum Zygomycota Barr, 1982
- Infraphylum Eumycota Cavalier-Smith, 1998 (Dikaryomycota)
- Superclass Microspora Sprague, 1982
- Class Microsporea Sprague, 1982
- Subclass Rudimicrosporia Sprague, 1977
- Subclass Microsporia Delphy, 1963
- Class Archaeascomycota
- Class Hemiascomycota
- Class Euascomycota
- Family Nephridiophagidae Sprague, 1970
- Superclass Mesomycetozoa Herr et al., 1999
- Superclass Choanoflagellata Kent, 1880
- Infraphylum Metazoa Haeckel, 1874
- Superclass Myxozoa Grassé, 1970
Adl et al. (2012) Edit
Adl, S.M. et al. (2012). The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–514, .
- Opisthokonta Cavalier-Smith 1987, emend. Adl et al. 2005
- Lang et al. 2002 (R)
- Ministeria Patterson et al. 1993, emend. Tong 1997 (Ministeriida Cavalier-Smith, 1997)
- Capsaspora Hertel et al. 2002 (Capsasporidae Cavalier-Smith 2008) (M)
- Amphibiocystidium ranae, Amphibiothecum penneri, Dermocystidium, Rhinosporidium seeberi, Sphaerothecum destruens
- Abeoforma whisleri, Amoebidium parasiticum, Anurofeca richardsi, Astreptonema, Caullerya mesnili, Creolimax fragrantissima, Eccrinidus flexilis, Enterobryus oxidi, Enteropogon sexuale, Ichthyophonus, Palavascia patagonica, Pseudoperkinsus tapetis, Psorospermium haeckeli, Sphaeroforma arctica
- Amoeboaphelidium, Aphelidium, Pseudoaphelidium [Pseudaphelidium]
- Astrosiga, Aulomonas, Choanoeca, Cladospongia, Codonocladium, Codonosigopsis, Codosiga (junior synonym Codonosiga), Desmarella (junior synonyms Codonodesmus and Kentrosiga), Dicraspedella, Diploeca, Diplosiga, Diplosigopsis, Kentia, Lagenoeca, Monosiga, Pachysoeca, Proterospongia, Salpingoeca, Salpingorhiza, Sphaeroeca, Stelexomonas, Stylochromonas
- Acanthoeca, Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta, Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina, Crucispina, Diaphanoeca, Didymoeca, Helgoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula, Platypleura, Pleurasiga, Polyfibula, Polyoeca, Saepicula, Saroeca, Savillea, Spinoeca, Spiraloecion, Stephanacantha, Stephanoeca, Syndetophyllum
- Shalchian-Tabrizi et al. 2008
- Mendoza et al. 2001 (Dermocystida Cavalier-Smith 1998) (R)
- Cavalier-Smith 1997, emend. Nitsche et al. 2011
- Grant 1836 (Parazoa Sollas 1884)
- Schmidt 1862 (Silicea Bowerbank 1864, emend. Gray 1867)
- Schmidt 1870 Sollas 1885, emend. Borchiellini et al. 2004
- Sperling et al. 2009, emend. Morrow et al. 2012 (R)
- Hartman 1958, emend. Borchiellini et al. 2004 (R) Hartman 1958, emend. Borchiellini et al. 2004 (R)
- Nuclearia Cienkowski 1865
- Fonticula Worley et al. 1979 (M)
- Rozella Cornu 1872 (= Rozellida Lara et al. 2010 Cryptomycota M. D. M. Jones & T. A. Richards 2011) R. T. Moore 1980
- Superkingdom Prokaryota
- Kingdom Archaea [= Archaebacteria]
- Kingdom Bacteria [= Eubacteria]
- Kingdom Protozoa
- Subkingdom Eozoa
- Infrakingdom Euglenozoa
- Infrakingdom Excavata
- Phylum Amoebozoa
- Phylum Choanozoa [with Microsporidia, Animalia, and Fungi constitutes "Supergroup Opisthokonta"]
- Phylum Microsporidia [with Choanozoa, Animalia, and Fungi constitutes "Supergroup Opisthokonta"]
- Phylum Sulcozoa
- Subkingdom Hacrobia
- Subkingdom Harosa [ /wiki/SAR" title="SAR">SAR"]
- Infrakingdom Halvaria
- Superphylum Alveolata
- Superphylum Heterokonta [ /wiki/Stramenopiles" title="Stramenopiles">Stramenopiles"]
- Subkingdom Dikarya [= Neomycota]
- Subkingdom Eomycota
- Subkingdom Biliphyta
- Subkingdom Viridiplantae
Toruella et al. (2015) Edit
Torruella, Guifré, et al. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology 25: 1–7, .
ASJC Scopus subject areas
Broadly sampled multigene trees of eukaryotes. / Yoon, Hwan Su Grant, Jessica Tekle, Yonas I. Wu, Min Chaon, Benjamin C. Cole, Jeffrey C. Logsdon, John M. Patterson, David J. Bhattacharya, Debashish Katz, Laura A.
Research output : Contribution to journal › Article › peer-review
T1 - Broadly sampled multigene trees of eukaryotes
AU - Bhattacharya, Debashish
N2 - Background. Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. Results. The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the 'Opisthokonta' receive strong support in our analyses. The supergroup 'Amoebozoa' has only moderate support, whereas the 'Chromalveolata', 'Excavata', 'Plantae', and 'Rhizaria' receive very limited or no support. Conclusion. Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the eukaryotic tree of life, which will be critical for resolving their phylogenetic interrelationships.
AB - Background. Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. Results. The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the 'Opisthokonta' receive strong support in our analyses. The supergroup 'Amoebozoa' has only moderate support, whereas the 'Chromalveolata', 'Excavata', 'Plantae', and 'Rhizaria' receive very limited or no support. Conclusion. Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the eukaryotic tree of life, which will be critical for resolving their phylogenetic interrelationships.
Opisthokonta is another widely diverse group of Protista including animal and fungus. Opisthokonta are flagellated cells that propel themselves with a single posterior flagellum, and do not contain an anterior flagella like most other eukaryote groups. The organisms consist of collagen as one of the main components of the extracellular matrix. The only discriminating characteristics of Opisthokonta are the platycristate mitochondria and flat, membrane-bound cavities that make a Golgi apparatus.
Choanoflagellates are a noteworthy clades of Opisthokonta if one is interested in marine invertebrates. Choanoflagellates are free-living unicellular and colonial eukaryotes. The choanocytes of choanocytes obsevered in Porifera.
We thank the Tara Oceans consortium and the people and sponsors who supported Tara Oceans. Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). This article is contribution number 117 of Tara Oceans. Computation time was provided by the SuperComputer System, Institute for Chemical Research, Kyoto University.
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Keywords : NCLDV, giant viruses, myosin, phylogeny, viral diversity, Nucleocytoviricota
Citation: Kijima S, Delmont TO, Miyazaki U, Gaia M, Endo H and Ogata H (2021) Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton. Front. Microbiol. 12:683294. doi: 10.3389/fmicb.2021.683294
Received: 20 March 2021 Accepted: 12 May 2021
Published: 07 June 2021.
Jonatas Abrahao, Federal University of Minas Gerais, Brazil
Rodrigo Araújo Lima Rodrigues, Federal University of Minas Gerais, Brazil
Philippe Colson, IHU Mediterranee Infection, France
Copyright © 2021 Kijima, Delmont, Miyazaki, Gaia, Endo and Ogata. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Os Opisthokonta são organismos eucariotas que formam um clado estritamente monofilético (um ramo evolutivo) no qual coexistem algumas formas unicelulares flageladas, inclui os reinos dos fungos verdadeiros (Fungi) e dos animais verdadeiros (Animalia).
- Filo Choanozoa (P)
- Classe Choanoflagellata (= Choanomonada)
- Classe Pluriformea
- Classe Mesomycetozoea (= Ichthyosporea)
- Classe Nucleariida
- Classe Ministeriida
O nome é uma alusão ao flagelo, singular quando está presente, e que ocupa uma posição posterior, fazendo avançar a célula para a frente dele, como se vê nos espermatozóides dos animais. Noutros ramos dos eucariotas em que ocorrem flagelos, estes são normalmente dois e situam-se à frente da célula durante o seu movimento. Nos grupos clássicos de fungos não existem fases flageladas, mas estas abundam em grupos tradicionalmente tratados como protistas, mas que agora se sabem que formam parte do mesmo clado.
Fazem parte do clado os seguintes táxons:
- Filo Choanozoa. Compreende vários grupos de protistas:
- (= Choanomonada), formas unicelulares móveis ou coloniais pedunculadas, dotadas de um colar, e que se alimentam como micrófagos filtradores. Semelhantes a certas células das esponjas, chamadas coanócitos. Provavelmente representam a forma original dos Opisthokonta, da qual derivariam os outros grupos. , que inclui um único organismo marinho não ciliado e saprófito encontrado na lagoa de um atol. (= Ichthyosporea), formas unicelulares flageladas ou amebóides, saprotróficas ou parasitas. (Nucleariida), um pequeno grupo de amebas que se encontram principalmente no solo e na água doce.
Fortes semelhanças entre Opisthokonta e Amoebozoa apoiam o seu agrupamento num clado denominado Unikonta.
- Infrakingdom Halvaria
- Subkingdom Eozoa
[Notes: M, monotypic group with only one described species P, paraphyletic group R, ribogroup assembled from phylogenetic studies.]
Karpov et al. (2014) Edit
Karpov, S. A., Mamkaeva, M. A., Aleoshin, V. V., Nassonova, E., Lilje, O., & Gleason, F. H. (2014). Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia. Frontiers in Microbiology, 5: 112. doi: 10.3389/fmicb.2014.00112.
Ruggiero et al. (2015) Edit
Ruggiero, M.A., Gordon, D.P., Orrell, T.M., Bailly, N., Bourgoin, T., Brusca, R.C., Cavalier-Smith, T., Guiry, M. D. & Kirk, P. M. (2015). A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248, .
- Class Microsporea Sprague, 1982
- Superclass Microspora Sprague, 1982
- Subphylum Fungi Nees,1817
- Class Archimycetes
- Phylum Opisthokonta
- (sluzave mreže) (uključene u supergrupu SAR) (sada u Amoebozoa) (vodene plijesni) (sada u supergrupi SAR)
- (bivše Trichomycete) (smatrane paratzitskim gljivama ili Sporozoa) (bivše Trichomycete) (ranije smatrane parazitskim gljivama incertae sedis)
Hoanoflagelati imaju kružni mitohondrijski DNK genom s dugim međugenskim regijama. Oko četiri puta je veći od životinjskih mitohondrijskih genoma i sadrži dvostruko više gena koji kodiraju proteine. Čini se da je Corallochytrium vjerovatno bliže gljivama nego životinjama, na osnovu prisustva ergosterola u membranama i sposobnosti za sintezu lizina putem puta AAA. Oblici sa ihtiosporama imaju deleciju dvije aminokiseline u svom genu EEF1A1, koji se smatra karakterističnim za gljive. Njihov genom je dug >200 kilobaznih pairova, sa nekoliko stotina linearnih hromosoma. U slijedećem filogenetskom stablu prikazano je koliko su se miliona miliona godina (Mya) kladusi razdvajali u novije grane. Stablo Holomycota prikazano je prema Tedersoo-u et al.  <
A subset of the amoebozoans, the slime molds, has several morphological similarities to fungi that are thought to be the result of convergent evolution. For instance, during times of stress, some slime molds develop into spore-generating fruiting bodies, much like fungi.
The slime molds are categorized on the basis of their life cycles into plasmodial or cellular types. Plasmodial slime molds are composed of large, multinucleate cells and move along surfaces like an amorphous blob of slime during their feeding stage (see the figure below). Food particles are lifted and engulfed into the slime mold as it glides along. Upon maturation, the plasmodium takes on a net-like appearance with the ability to form fruiting bodies, or sporangia, during times of stress. Haploid spores are produced by meiosis within the sporangia, and spores can be disseminated through the air or water to potentially land in more favorable environments. If this occurs, the spores germinate to form ameboid or flagellate haploid cells that can combine with each other and produce a diploid zygotic slime mold to complete the life cycle.
The life cycle of the plasmodial slime mold is shown. The brightly colored plasmodium in the inset photo is a single-celled, multinucleate mass. (credit: modification of work by Dr. Jonatha Gott and the Center for RNA Molecular Biology, Case Western Reserve University)
The cellular slime molds function as independent amoeboid cells when nutrients are abundant (see the figure below). When food is depleted, cellular slime molds pile onto each other into a mass of cells that behaves as a single unit, called a slug. Some cells in the slug contribute to a 2–3-millimeter stalk, drying up and dying in the process. Cells atop the stalk form an asexual fruiting body that contains haploid spores. As with plasmodial slime molds, the spores are disseminated and can germinate if they land in a moist environment. One representative genus of the cellular slime molds is Dictyostelium, which commonly exists in the damp soil of forests.
Cellular slime molds may exist as solitary or aggregated amoebas. (credit: modification of work by “thatredhead4”/Flickr)
You can view this video to see the formation of a fruiting body by a cellular slime mold.
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Gams, H. (1947). Die Protochlorinae als autotrophe Vorfahren von Pilzen und Tieren? Mikroskopie, 2, 383–7, . From Leadbeater (2015) and Copeland (1956).
Rothmaler (1951) Edit
Rothmaler, Werner. (1951). Die Abteilungen und Klassen der Pflanzen. Feddes Rep Spec Nov Reg Veg 3: 256–266, , .
- Rothm. (1948) – Protozoa Owen (1860) – Protista Haeckel (1866) emend. Barkley (1939) – Protoctista Hogg (1861)
- Pascher (1931) – Inophyta Haeckel (1866) – PhaeophytaMycophytina Rothm. (1949) [?]
- Rothm., nom. nov. – Archimycetes A. Fischer (1894) – Opisthocontae Gams (1947) – Protochlorinae Vischer (1945) – Opisthophyceae Rothm., nom. event. – Archemycetae Barkley (1939)
Copeland (1956) Edit
Copeland, H. F. (1956). The Classification of Lower Organisms. Palo Alto: Pacific Books, .