Detlef D. Leipe

Small subunit ribosomal RNA+ of Hexamita inflata and the quest for the first branch in the eukaryotic tree

A phylogenetic analysis of the small subunit ribosomal RNA (16S-like rRNA) coding region from Hexamita inflata demonstrates that parasitism alone cannot explain early diverging eukaryotic lineages. Parasitic and free-living diplomonads, as well as trichomonads and microsporidia, diverge at the base of the eukaryotic tree. The relative branching order of diplomonads, trichomonads and microsporidia is influenced by outlying prokaryotic taxa with different G+C compositions in their rRNA coding regions. The high G+C prokaryotes position Giardia lamblia at the base of the eukaryotic tree but split diplomonads into a paraphyletic group. When the outlying groups are restricted to rRNAs with nominal G+C compositions, diplomonads form a monophyletic group that diverged after the microsporidia and trichomonads. This unstable branching pattern correlates with unusual nucleotide compositions in the rRNAs of G. lamblia (75% G+C) and Vairimorpha necatrix (35% G+C). In contrast, the 51% G+C composition of the H. inflata rRNA is typical of other eukaryotic rRNAs. Its divergence after trichomonads is strongly supported by bootstrap replicates in distance analyses that do not include G. lamblia. Because of a low G+C composition in its rRNA coding region, the phylogenetic placement of V. necatrix is uncertain and the identity of the deepest branching eukaryotic lineage is ambiguous.

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons.

Phylogeny of trichomonads inferred from small-subunit rRNA sequences.

ABSTRACT. Small subunit (16S‐like) ribosomal RNA sequences were obtained from representatives of all four families constituting the order Trichomonadida. Comparative sequence analysis revealed that the Trichomonadida are a monophyletic lineage and a deep branch of the eukaryotic tree. Relative to other early divergent eukaryotic assemblages the branching pattern within the Trichomonadida is very shallow. This pattern suggests the Trichomonadida radiated recently, perhaps in conjunction with their animal hosts. From a morphological perspective the Devescovinidae and Calonymphidae are considered more derived than the Monocercomonadidae and Trichomonadidae. Molecular trees inferred by distance, parsimony and likelihood techniques consistently show the Devescovinidae and Calonymphidae are the earliest diverging lineages within the Trichomonadida, however bootstrap values do not strongly support a particular branching order. In an analysis of all known 16S‐like ribosomal RNA sequences, the Trichomonadida share most recent common ancestry with unidentified protists from the hindgut of the termite Reticulitermes flavipes. The position of two putative free‐living trichomonads in the tree is indicative of derivation from symbionts rather than direct descent from some free‐living ancestral trichomonad.

16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis, and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group

Summary A phylogenetic analysis of the 16S-like ribosomal RNA coding regions from Labyrinthuloides haliotidis, Developayella elegans, Proteromonas lacertae and other organisms corroborates morphological evidence that proteromonads and other eukaryotes with tripartite tubular hairs form a monophyletic group of organisms, the stramenopiles. Within the stramenopiles, the heterotrophic groups (proteromonads, Labyrinthulida, bicosoecids, Developayella and oomycetes) diverge before the radiation of the “heterokont algae”, the autotrophic stramenopiles. The stramenopiles were initially “protozoan” but their ecological success is largely attributable to the late symbiotic acquisition of chloroplasts. The stramenopiles and other taxa with chlorophyll a+c containing chloroplasts (cryptomonads, dinoflagellates, and haptophytes) do not share a common autotrophic ancestor. These photosynthetic assemblages acquired their plastids independently.

Insights into the Evolution of Nuclear Dualism in the Ciliates Revealed by Phylogenetic Analysis of rRNA Sequences

The small subunit rRNA gene sequences of the karyorelictean ciliates, Loxodes striatus and Protocruzia sp., and the heterotrichian ciliates, Climacostomum virens and Eufolliculina uhligi, were used to test the evolution of nuclear dualism in the Phylum Ciliophora. Phylogenies derived using a least squares distance method, neighbour joining, and maximum parsimony demonstrate that the karyorelictean ciliates sensu Small and Lynn, 1985 do not form a monophyletic group. However, Loxodes and the heterotrich ciliates form the first branch in the ciliate lineage, and Protocruzia branches, in distance methods, basal to the spirotrich lineage. It is proposed that Protocruzia be removed from the Class Karyorelictea, and placed in closer taxonomic association with the spirotrich lineage. The distribution of nuclear division types along the phylogenetic tree is consistent with the notion that macronuclei incapable of division represent a derived rather than a primitive or “karyorelictid” character trait.

Phylogenetic analysis of complete small subunit ribosomal RNA coding region of Myxidium lieberkuehni: evidence that Myxozoa are Metazoa and related to the Bilateria.

Summary: The phylogenetic position of Myxozoa relative to other eukaryotes has been controversialDuring their complex life cycles they show both protist and metazoan charactersIn contrast to their general classification as protists, phylogenetic comparisons of the complete 16Slike rRNA sequence of the myxosporean Myxidium lieberkuehni with other, unicellular and metazoan sequences show that Myxozoa share a common evolutionary history with Metazoa and are most closely related to the Bilateria

Evolution of 16S-like ribosomal RNA genes in the ciliophoran taxa litostomatea and phyllopharyngea

Summary Complete small subunit (16S-like rRNA) gene sequences were determined for two litostome ( Homalozoon vermiculare and Loxophyllum utriculariae ) and two phyllopharyngean ciliates ( Discophrya collini and Trithigmostoma steini ). Six of the eight ciliate classes are now represented in the 16S-like rRNA data base. Phylogenetic reconstructions identify Blepharisma americanum as the first ciliate branch but the heterotrichs B. americanum and Metopus palaeformis do not appear to be closely related. Later branching ciliate lineages are represented by the litostomes, spirotrichs and a heterogeneous group that includes colpodid, oligohymenophoran, and phyllopharyngean ciliates. The relatively simple cytostomal organization of litostomes and phyllopharyngeans should not be regarded as primitive states. Using the rRNA phylogenies as framework to understand the evolution of non-molecular features, the low complexity of their oral structures can be interpreted as a secondary adaptation — possibly caused by a shift towards macro-phagous feeding behavior.

Phylogenetic Relationships of the Nassulida Within the Phylum Ciliophora Inferred from the Complete Small Subunit rRNA Gene Sequences of Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius

ABSTRACT. Using comparisons of complete small subunit rRNA sequences from the ciliated protozoans Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius we inferred the phylogenetic position of the Nassulida (Class Nassophorea) within the Ciliophora. In distance matrix analyses the Nassulida share a common ancestry with the colpodean ciliate Colpoda inflata. Distance matrix and parsimony methods convincingly demonstrate that the Nassulida plus Colpodida are members of a complex ciliate assemblage that also includes the oligohymenophorans and phyllopharyngeans. These phylogenetic inferences are largely congruent with recent analyses of 23S‐like rRNA gene sequences and morphogenetic features. Groups traditionally thought to represent ancestral lineages now appear as highly derived ciliates. In contrast, heterotrichs which were considered to represent a highly evolved group, diverge at the base of the ciliates.

A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain

BackgroundRecent sequence-structure studies on P-loop-fold NTPases have substantially advanced the existing understanding of their evolution and functional diversity. These studies provide a framework for characterization of novel lineages within this fold and prediction of their functional properties.ResultsUsing sequence profile searches and homology-based structure prediction, we have identified a previously uncharacterized family of P-loop NTPases, which includes the neuronal membrane protein and receptor tyrosine kinase substrate Kidins220/ARMS, which is conserved in animals, the F-plasmid PifA protein involved in phage T7 exclusion, and several uncharacterized bacterial proteins. We refer to these (predicted) NTPases as the KAP family, after Kidins220/ARMS and PifA. The KAP family NTPases are sporadically distributed across a wide phylogenetic range in bacteria but among the eukaryotes are represented only in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side. We show that the KAP family belongs to the same major division of the P-loop NTPase fold with the AAA+, ABC, RecA-like, VirD4-like, PilT-like, and AP/NACHT-like NTPase classes. In addition to the KAP family, we identified another small family of predicted bacterial NTPases, with two transmembrane helices inserted into the P-loop domain. This family is not specifically related to the KAP NTPases, suggesting independent acquisition of the transmembrane helices.ConclusionsWe predict that KAP family NTPases function principally in the NTP-dependent dynamics of protein complexes, especially those associated with the intracellular surface of cell membranes. Animal KAP NTPases, including Kidins220/ARMS, are likely to function as NTP-dependent regulators of the assembly of membrane-associated signaling complexes involved in neurite growth and development. One possible function of the prokaryotic KAP NTPases might be in the exclusion of selfish replicons, such as viruses, from the host cells. Phylogenetic analysis and phyletic patterns suggest that the common ancestor of the animals acquired a KAP NTPase via lateral transfer from bacteria. However, an earlier transfer into eukaryotes followed by multiple losses in several eukaryotic lineages cannot be ruled out.

HYPERAMOEBA ISOLATED FROM HUMAN FECES : DESCRIPTION AND PHYLOGENETIC AFFINITY

Summary The morphology and phylogenetic affinity of Hyperamoeba isolated from human feces is described. During its life cycle, it switches reversibly from flagellate to aflagellated amoebae and is capable of forming cysts. It grows aerobically. Under anaerobic conditions it persists but does not replicate. The amoeboflagellate has a single nucleus with a distinct nucleolus. Its mitochondria possess tubular cristae and a central electron dense body, similar to that of plasmodial slime molds. A single contractile vacuole is evident. The flagellate has one detectable anterior flagellum but two basal bodies are visible at the ultrastructure level. The flagellar apparatus is very similar to that found in some Eumycetozoa, especially the myxogastrids. The uninucleate cyst has a bi-layered endocyst and a membranous, irregular shaped, faintly laminated ectocyst that harbors bacterial inclusions. Phylogenetic reconstructions based on nuclear small subunit ribosomal gene sequence comparisons show that Hyperamoeba is closely related to the plasmodial slime mold Physarum polycephalum. These protists share a most recent common ancestry that excludes all other taxa in the database. This phylogenetic relationship is supported by detailed similarities in both mitochondrial and flagellar apparatus ultrastructure.