Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase

The Amoebozoa

The model organism Dictyostelium discoideum is a member of the Amoebozoa, one of the six major -divisions of eukaryotes. Amoebozoa comprise a wide variety of amoeboid and flagellate organisms with single cells measuring from 5 μm to several meters across. They have adopted many different life styles and sexual behaviors and can live in all but the most extreme environments. This chapter provides an overview of Amoebozoan diversity and compares roads towards multicellularity within the Amoebozoa with inventions of multicellularity in other protist divisions. The chapter closes with a scenario for the evolution of Dictyostelid multicellularity from an Amoebozoan stress response.

Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications

The taxon Heterolobosea (Excavata) is a major group of protists well known for its diversity of life stages. Most are amoebae capable of transforming into flagellates (amoeboflagellates), while others are known solely as flagellates or solely as amoebae. The deepest-branching heterolobosean taxon confirmed previously, Pharyngomonas, was generally assumed to be a pure flagellate, suggesting that the amoeba form arose later in the evolution of Heterolobosea sensu lato. Here we report that multiple isolates of Pharyngomonas are actually amoeboflagellates that also have cyst stages, with only amoebae transforming into cysts. The amoeba form of Pharyngomonas showed heterolobosean characteristics (e. g. eruptive movement), but also possessed unusual morphological features like slow-flowing crenulated hyaline crescents with conical subpseudopodia, finger-like projections and branching posterior extensions. Furthermore, phylogenetic analyses of 18S ribosomal RNA gene sequences that included two undescribed species of amoebae showed that Pharyngomonas is not the only deep-branching heterolobosean to possess an amoeba stage. These results suggest that possession of an amoeba stage was ancestral for Heterolobosea, unifying this taxon as a group of species with amoeba stages in their lifecycle or derived from organisms with such stages.

Evolution and diversity of dictyostelid social amoebae

Dictyostelid social amoebae are a large and ancient group of soil microbes with an unusual multicellular stage in their life cycle. Taxonomically, they belong to the eukaryotic supergroup Amoebozoa, the sister group to Opisthokonta (animals + fungi). Roughly half of the ~150 known dictyostelid species were discovered during the last five years and probably many more remain to be found. The traditional classification system of Dictyostelia was completely overturned by cladistic analyses and molecular phylogenies of the past six years. As a result, it now appears that, instead of three major divisions there are eight, none of which correspond to traditional higher-level taxa. In addition to the widely studied Dictyostelium discoideum, there are now efforts to develop model organisms and complete genome sequences for each major group. Thus Dictyostelia is becoming an excellent model for both practical, medically related research and for studying basic principles in cell-cell communication and developmental evolution. In this review we summarize the latest information about their life cycle, taxonomy, evolutionary history, genome projects and practical importance.

A contemporary evaluation of the acrasids (Acrasidae, Heterolobosea, Excavata)

Sorocarpic protists are organisms that individually aggregate and work together to form a fungus-like fruiting body (sorocarp). The amoeboid forms are often colloquially referred to as "cellular slime molds" or "acrasids". We argue the latter term should be used only to refer to members of Acrasidae in Heterolobosea. Here we study the diversity of two Acrasidae genera, Acrasis and the closely similar Pocheina, using a combination of morphological characteristics and small subunit rRNA gene sequences. A total of eight isolates of Acrasis and an example of Pocheina were examined. Acrasis/Pocheina form a well-supported monophyletic group that is the highly supported sister to a clade containing Allovahlkampfia and several other amoebae. Four molecular lineages of Acrasis were resolved, each of which is characterized by a distinctive fruiting body morphology. Each lineage represents a species, two of which are novel, Acrasis kona n. sp. and Acrasis takarsan n. sp. An isolate identified as Pocheina rosea is nested within the clade containing isolates of the taxon Acrasis rosea, into which P. rosea is tentatively subsumed. One member of the tightly knit allovahlkampfid clade was induced to form a simple sorocarp, leading us to include this clade in Acrasidae.

Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes

Background

Although capable to evolve, viruses are generally considered non-living entities because they are acellular and devoid of metabolism. However, the recent publication of the genome sequence of the Mimivirus, a giant virus that parasitises amoebas, strengthened the idea that viruses should be included in the tree of life. In fact, the first phylogenetic analyses of a few Mimivirus genes that are also present in cellular lineages suggested that it could define an independent branch in the tree of life in addition to the three domains, Bacteria, Archaea and Eucarya.

Results

We tested this hypothesis by carrying out detailed phylogenetic analyses for all the conserved Mimivirus genes that have homologues in cellular organisms. We found no evidence supporting Mimivirus as a new branch in the tree of life. On the contrary, our phylogenetic trees strongly suggest that Mimivirus acquired most of these genes by horizontal gene transfer (HGT) either from its amoebal hosts or from bacteria that parasitise the same hosts. The detection of HGT events involving different eukaryotic donors suggests that the spectrum of hosts of Mimivirus may be larger than currently known.

Conclusion

The large number of genes acquired by Mimivirus from eukaryotic and bacterial sources suggests that HGT has been an important process in the evolution of its genome and the adaptation to parasitism.

Mitochondria of Protists

Over the past several decades, our knowledge of the origin and evolution of mitochondria has been greatly advanced by determination of complete mitochondrial genome sequences. Among the most informative mitochondrial genomes have been those of protists (primarily unicellular eukaryotes), some of which harbor the most gene-rich and most eubacteria-like mitochondrial DNAs (mtDNAs) known. Comparison of mtDNA sequence data has provided insights into the radically diverse trends in mitochondrial genome evolution exhibited by different phylogenetically coherent groupings of eukaryotes, and has allowed us to pinpoint specific protist relatives of the multicellular eukaryotic lineages (animals, plants, and fungi). This comparative genomics approach has also revealed unique and fascinating aspects of mitochondrial gene expression, highlighting the mitochondrion as an evolutionary playground par excellence.

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large data set containing 123 genes for representatives of three phenotypically highly divergent major amoeboid lineages: Pelobionta, Entamoebidae, and Mycetozoa. Phylogenetic reconstruction was performed on approximately 25,000 aa positions for 30 species by using maximum-likelihood approaches. All well-established eukaryotic groups were recovered with high statistical support, validating our approach. Interestingly, the three amoeboid lineages strongly clustered together in agreement with the Conosa hypothesis [as defined by T. Cavalier-Smith (1998) Biol. Rev. Cambridge Philos. Soc. 73, 203-266]. Two amitochondriate amoebae, the free-living Mastigamoeba and the human parasite Entamoeba, formed a significant sister group to the exclusion of the mycetozoan Dictyostelium. This result suggested that a part of the reductive process in the evolution of Entamoeba (e.g., loss of typical mitochondria) occurred in its free-living ancestors. Applying this inexpensive expressed sequence tag approach to many other lineages will surely improve our understanding of eukaryotic evolution.

SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited

Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for the amoeboid lineages and an extraordinary diversity of amoebae species. Molecular data, however, exist only for a few species of the numerous taxa belonging to this group. Here, we present the small-subunit (SSU) rDNA sequences of four species of typical large gymnamoebae: Amoeba proteus, Amoeba leningradensis, Chaos nobile, and Chaos carolinense. Sequence analysis suggests that the four species are closely related to the species of genera Saccamoeba, Leptomyxa, Rhizamoeba, Paraflabellula, Hartmannella, and Echinamoeba. All of them form a relatively well-supported clade, which corresponds to the subclass Gymnamoebia, in agreement with morphology-based taxonomy. The other gymnamoebae cluster in small groups or branch separately. Their relationships change depending on the type of analysis and the model of nucleotide substitution. All gymnamoebae branch together in Neighbor-Joining analysis with corrections for among-site rate heterogeneity and proportion of invariable sites. This clade, however, is not statistically supported by SSU rRNA gene sequences and further analysis of protein sequence data will be necessary to test the monophyly of gymnamoebae.

Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies

Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondrial protists. They share ultrastructural similarities with eukaryotes that occupy basal positions in molecular phylogenies, and their mitochondrial genome architecture is eubacterial-like, suggesting a close affinity with the ancestral alpha-proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. To elucidate relationships among jakobids and other early-diverging eukaryotic lineages, we characterized alpha- and beta-tubulin genes from four jakobids: Jakoba libera, Jakoba incarcerata, Reclinomonas americana (the "core jakobids"), and Malawimonas jakobiformis. These are the first reports of nuclear genes from these organisms. Phylogenies based on alpha-, beta-, and combined alpha- plus beta-tubulin protein data sets do not support the monophyly of the jakobids. While beta-tubulin and combined alpha- plus beta-tubulin phylogenies showed a sister group relationship between J. libera and R. americana, the two other jakobids, M. jakobiformis and J. incarcerata, had unclear affinities. In all three analyses, J. libera, R. americana, and M. jakobiformis emerged from within a well-supported large "plant-protist" clade that included plants, green algae, cryptophytes, stramenopiles, alveolates, Euglenozoa, Heterolobosea, and several other protist groups, but not animals, fungi, microsporidia, parabasalids, or diplomonads. A preferred branching order within the plant-protist clade was not identified, but there was a tendency for the J. libera-R. americana lineage to group with a clade made up of the heteroloboseid amoeboflagellates and euglenozoan protists. Jakoba incarcerata branched within the plant-protist clade in the beta- and the combined alpha- plus beta-tubulin phylogenies. In alpha- tubulin trees, J. incarcerata occupied an unresolved position, weakly grouping with the animal/fungal/microsporidian group or with amitochondriate parabasalid and diplomonad lineages, depending on the phylogenetic method employed. Tubulin gene phylogenies were in general agreement with mitochondrial gene phylogenies and ultrastructural data in indicating that the "jakobids" may be polyphyletic. Relationships with the putatively deep-branching amitochondriate diplomonads remain uncertain.

Functional genomic analysis reveals the utility of the I/LWEQ module as a predictor of protein:actin interaction

The I/LWEQ module is a conserved sequence that we have identified as an actin-binding motif in the metazoan focal adhesion protein talin and the yeast protein Sla2p. Both of these proteins are associated with the actin cytoskeleton in cells. To better establish the value of the I/LWEQ module for prediction of actin-binding function, we have applied a functional genomics approach. Analysis of the 23 available I/LWEQ module sequences supports the division of I/LWEQ protein superfamily into four groups: (1) metazoan talin, (2) Dictyostelium discoideum talin homologs TalA/B, (3) metazoan Hip1p, and (4) yeast Sla2p. We show here that I/LWEQ modules from each major group bind to F-actin in vitro and that GFP-fusion proteins of the I/LWEQ modules of talin and Sla2p bind to F-actin in vivo. Therefore, the presence of an I/LWEQ module is strongly predictive of protein-actin interactions. The structural and functional conservation of the I/LWEQ module across the phylogenetic distance between cellular slime molds and mammals implies that the role of the I/LWEQ module is to connect diverse proteins involved in distinct cellular processes, including cell adhesion, cytoskeletal organization, and cell differentiation, to the actin cytoskeleton.

A Search for the Origins of Animals and Fungi: Comparing and Combining Molecular Data

Green plants, animals, and fungi have long held our interest as complex, largely multicellular eukaryotes of indeterminate origin. Considerable progress has now been made toward understanding the evolutionary relationships among these taxa as well as identifying their closest protistan relatives. An exclusive animal-fungal clade (the Opisthokonta) is now widely accepted based on an insertion in the protein synthesis elongation factor 1alpha (EF-1alpha) and molecular phylogenies of ribosomal RNAs and the conservative proteins actin, alpha-tubulin, beta-tubulin, and EF-1alpha. Protein data also suggest that the cellular (dictyostelid) and acellular (myxogastrid) slime molds are a close outgroup to the animal-fungal clade. Subsequent sequencing and phylogenetic analysis of EF-1alpha sequences very strongly support a monophyletic slime mold clade (the Mycetozoa or Eumycetozoa), which also includes the lesser-known protostelid slime molds. Monophyly of the opisthokont and mycetozoan clades, exclusive of green plants, is suggested by individual analyses of EF-1alpha and actin and given strong support by concatenated protein data. Neither the monophyly of the slime molds nor their close relationship to animals and fungi are consistently supported by ribosomal RNA data. Thus, it appears unlikely that any single molecule will accurately reconstruct all higher-order taxonomy.

Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family

Trichomonads, together with diplomonads and microsporidia, emerge at the base of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny. However, phylogenies based on protein sequences such as tubulin are markedly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could be a reliable phylogenetic marker. In eukaryotes, HSP70s are found in cytosol, endoplasmic reticulum, and organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly complete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitochondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters considered. Almost all the undoubtedly monophyletic groups, defined by ultrastructural characters, were recovered. However, due to the long branch attraction phenomenon, the evolutionary rates were the main factor determining the position of species, even with the use of a close outgroup, which is an important advantage of HSP70 with respect to many other markers. Numerous variable sites are peculiar to Trichomonas and probably generated the artefactual placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of species; and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.

Glyceraldehyde-3-phosphate dehydrogenase from Tetrahymena pyriformis: enzyme purification and characterization of a gapC gene with primitive eukaryotic features

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC.1.2.1.12) was purified to electrophoretic homogeneity from an amicronucleated strain of the ciliate Tetrahymena pyriformis using a three-step procedure. The native enzyme is an homotetramer of 145 kDa exhibiting absolute specificity for NAD. In its catalytic properties it is similar to other glycolytic GAPDHs. Chromatofocusing analysis showed the presence of only one basic GAPDH isoform with an isoelectric point of 8.8. Western blots using a monospecific polyclonal antibody raised against the T. pyriformis GAPDH showed a single 36-kDa band corresponding to the enzyme subunit in the cytosolic protein fraction of this strain and the closely related species, both from the class Oligohymenophorea, Paramecium tetraurelia. No bands were immunodetected in the ciliate Colpoda inflata (class Colpodea) and in the diverse eukaryotes and eubacteria tested. A 0.5-kb DNA fragment which corresponds to an internal region of a gapC gene was generated by polymerase chain reaction using cDNA of T. pyriformis as template. This gene codes for a basic GAPDH protein with eukaryotic-diplomonad signatures and exhibits a codon usage biased in the manner typical for T. pyriformis genes. Southern blots performed both under homologous and heterologous conditions using this amplified cDNA fragment as a probe, indicated that it should be the only gapC gene present in the macronuclear genome of this ciliate, its expression being confirmed by Northern blot analysis. These results are discussed in connection with the peculiar genomic organization of ciliates and in the context of protist evolution.

The tigA gene is a transcriptional fusion of glycolytic genes encoding triose-phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase in oomycota

Genes encoding triose-phosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are fused and form a single transcriptional unit (tigA) in Phytophthora species, members of the order Pythiales in the phylum Oomycota. This is the first demonstration of glycolytic gene fusion in eukaryotes and the first case of a TPI-GAPDH fusion in any organism. The tigA gene from Phytophthora infestans has a typical Oomycota transcriptional start point consensus sequence and, in common with most Phytophthora genes, has no introns. Furthermore, Southern and PCR analyses suggest that the same organization exists in other closely related genera, such as Pythium, from the same order (Oomycota), as well as more distantly related genera, Saprolegnia and Achlya, in the order Saprolegniales. Evidence is provided that in P. infestans, there is at least one other discrete copy of a GAPDH-encoding gene but not of a TPI-encoding gene. Finally, a phylogenetic analysis of TPI does not place Phytophthora within the assemblage of crown eukaryotes and suggests TPI may not be particularly useful for resolving relationships among major eukaryotic groups.

Origin and evolution of the slime molds (Mycetozoa)

The Mycetozoa include the cellular (dictyostelid), acellular (myxogastrid), and protostelid slime molds. However, available molecular data are in disagreement on both the monophyly and phylogenetic position of the group. Ribosomal RNA trees show the myxogastrid and dictyostelid slime molds as unrelated early branching lineages, but actin and beta-tubulin trees place them together as a single coherent (monophyletic) group, closely related to the animal-fungal clade. We have sequenced the elongation factor-1alpha genes from one member of each division of the Mycetozoa, including Dictyostelium discoideum, for which cDNA sequences were previously available. Phylogenetic analyses of these sequences strongly support a monophyletic Mycetozoa, with the myxogastrid and dictyostelid slime molds most closely related to each other. All phylogenetic methods used also place this coherent Mycetozoan assemblage as emerging among the multicellular eukaryotes, tentatively supported as more closely related to animals + fungi than are green plants. With our data there are now three proteins that consistently support a monophyletic Mycetozoa and at least four that place these taxa within the "crown" of the eukaryote tree. We suggest that ribosomal RNA data should be more closely examined with regard to these questions, and we emphasize the importance of developing multiple sequence data sets.