Major Eukaryotic Groups Research Articles

Phylogenetic Position of Blastocystis hominis and of Stramenopiles Inferred from Multiple Molecular Sequence Data

Blastocystis hominis, a parasite of the human intestine, has recently been positioned within stramenopiles by the small subunit rRNA phylogeny. To further confirm its phylogenetic position using multiple molecular sequence data, we determined the nucleotide sequences putatively encoding small subunit ribosomal RNA, cytosolic-type 70-kDa heat shock protein, translation elongation factor 2, and the non-catalytic 'B' subunit of vacuolar ATPase of B. hominis (HE87-1 strain). Moreover, we determined the translation elongation factor 2 sequence of an apicomplexan parasite, Plasmodium falciparum, that belongs to alveolates. The maximum likelihood analyses of small subunit rRNA and cytosolic-type 70-kDa heat shock protein clearly demonstrated that B. hominis (HE87-1 strain) is positioned within stramenopiles, being congruent with the previous small subunit rRNA analysis, including the sequences of B. hominis (Nand strain) and a Blastocystis isolate from guinea pig. Although no clear resolution among major eukaryotic groups was obtained by the individual phylogenies based on the four molecules analyzed here, a combined analysis of various molecules, including these, clearly indicated that Blastocystis/stramenopiles are the closest relatives of alveolates.

A Cyanobacterial Gene in Nonphotosynthetic Protists—An Early Chloroplast Acquisition in Eukaryotes?

Since the incorporation of mitochondria and chloroplasts (plastids) into the eukaryotic cell by endosymbiosis [1], genes have been transferred from the organellar genomes to the nucleus of the host [2–4], via an ongoing process known as endosymbiotic gene transfer [5]. Accordingly, in photosynthetic eukaryotes, nuclear genes with cyanobacterial affinity are believed to have originated from endosymbiotic gene transfer from chloroplasts. Analysis of the Arabidopsis thaliana genome has shown that a significant fraction (2%–9%) of the nuclear genes have such an endosymbiotic origin [3]. Recently, it was argued that 6-phosphogluconate dehydrogenase (gnd)—the second enzyme in the oxidative pentose phosphate pathway—was one such example [6]. Here we show that gnd genes with cyanobacterial affinity also are present in several nonphotosynthetic protistan lineages, such as Heterolobosea, Apicomplexa, and parasitic Heterokonta. Current data cannot definitively resolve whether these groups acquired the gnd gene by primary and/or secondary endosymbiosis or via an independent lateral gene transfer event. Nevertheless, our data suggest that chloroplasts were introduced into eukaryotes much earlier than previously thought and that several major groups of heterotrophic eukaryotes have secondarily lost photosynthetic plastids.

Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?

In recent years, the increased sampling of protein-coding genes from diverse eukaryotes has revealed that many aspects of each gene tree are at odds with other phylogenies. This has led to the belief that each gene tree has unique strengths and weaknesses, suggesting that an accurate picture of eukaryotic relationships will be achieved only through comparative phylogeny using several different genes. To this end, actin genes were characterized from two genera of chlorarachniophytes, Chlorarachnion and Lotharella, and three species of the cercomonad flagellate Cercomonas: Phylogenetic trees including these new actin genes confirm the recently proposed relationship between chlorarachniophytes and cercomonads (Cercozoa) and, more importantly, also show a close relationship between Cercozoa and Foraminifera. Both of these are major eukaryotic groups encompassing extremely diverse organisms, yet there is no strong evidence for the evolutionary position of either from morphological or molecular data. The union of Cercozoa and Foraminifera suggested by actin phylogeny represents a novel step in the long process of determining the broad relationships between all major eukaryotic groups.

Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most-parsimonious trees, and finding them all may be impossible using convential phylogenetic methods. To examine the reliability of the number and relationships of eukaryotic kingdoms proposed by previous analyses of the SSU, we calculated trees from aligned sequences from eukaryotes in the Ribosomal Database Project using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups. Two separate analyses were carried out: an analysis in which all bases were equally weighted, and one in which transversions only were used. The parsimony jackknife procedure was able to efficiently find trees in which most major groups of eukaryotes were supported and in which some evolutionary hypotheses proposed by previous workers were tested. The relationships of these major groups to each other were largely unresolved, indicating that the SSU data, as represented in this database, is insufficient for answering questions about these deep branches. Interestingly, the analysis of transitions differs from the results of the entire data set, primarily being less resolved. This indicates that transversional mutations are important contributors to the resolved structure of the tree.

Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes.

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most-parsimonious trees, and finding them all may be impossible using convential phylogenetic methods. To examine the reliability of the number and relationships of eukaryotic kingdoms proposed by previous analyses of the SSU, we calculated trees from aligned sequences from eukaryotes in the Ribosomal Database Project using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups. Two separate analyses were carried out: an analysis in which all bases were equally weighted, and one in which transversions only were used. The parsimony jackknife procedure was able to efficiently find trees in which most major groups of eukaryotes were supported and in which some evolutionary hypotheses proposed by previous workers were tested. The relationships of these major groups to each other were largely unresolved, indicating that the SSU data, as represented in this database, is insufficient for answering questions about these deep branches. Interestingly, the analysis of transitions differs from the results of the entire data set, primarily being less resolved. This indicates that transversional mutations are important contributors to the resolved structure of the tree.

New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences.

The current framework of the eukaryotic phylogeny is based on the analysis of a comprehensive set of sequences of the small subunit ribosomal RNA. However, phylogenies based on protein-encoding genes are not completely congruent with this picture. Since congruence between different markers is the best tool to determine evolutionary history, we focused on Hsp70 (heat-shock protein of 70 kDa), a chaperone protein which is highly conserved and is a potentially reliable phylogenetic marker. We used a PCR-based approach to sequence Hsp70s in two distinct classes of Ciliates. Seven Hsp70s were identified from Paramecium tetraurelia (Oligohymenophora) and six Hsp70s from Euplotes aediculatus (Hypotricha), encompassing orthologous genes for all major Hsp70 classes of Eukaryotes, i.e., those localized in cytosol, in endoplasmic reticulum, and in mitochondria. Three independent phylogenies of eukaryotes, based on each set of orthologous genes, have been constructed using different tree reconstruction methods. A significant advantage of Hsp70s is the existence of outgroups close to Eukaryotes for these major classes, reducing the long-branch attraction artifact due to the outgroup. The monophyly of Ciliates is supported by good bootstrap proportions in the phylogenetic reconstructions, and this phylum is generally a sister-group of Sporozoa, forming the expected Alveolates clade. The Hsp70 seems to be a suitable phylogenetic marker since it recovers all the monophyletic groups, undoubtedly defined by morphological criteria. The Hsp70 trees are, however, notably different from the rRNA ones and do not show two aspects of the classical topology, i.e., the successive emergence of deeply branching groups and the vast assembly of the major eukaryotic groups, emerging at the tip of the tree, i.e., the "terminal crown". More precisely, the Hsp70 trees do not resolve the relationships between the major groups of Eukaryotes with confidence, in keeping with the hypothesis that all these groups emerged in a great radiation that occurred at the origin of all the extant Eukaryotes.

Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote.

We have sequenced the small ribosomal subunit RNA gene of the diplozoan Trepomonas agilis. This provides the first molecular information on a free-living archezoan. We have performed a phylogenetic analysis by maximum likelihood, parsimony, and distance methods for all available nearly complete archezoan small subunit ribosomal RNA genes and for representatives of all major groups of more advanced eukaryotes (metakaryotes). These show Diplozoa as the earliest-diverging eukaryotic lineage, closely followed by microsporidia. Trepomonas proves to be much more closely related to Hexamita, and, to a lesser degree, to Spironucleus, than to Giardia. The close relationship between the free-living Trepomonas on our trees and the parasites Hexamita inflata and Spironucleus refutes the idea that the early divergence of the amitochondrial Archezoa is an artefact caused by parasitism. The deep molecular divergence between the three phagotrophic genera with two cytostomes (Hexamita, Trepomonas, Spironucleus) and the saprotrophic Giardia that lacks cytostomes is in keeping with the classical evidence for a fundamental difference in the symmetry of the cytoskeleton between the two groups. We accordingly separate the two groups as two orders: Distomatida for those with two cytostomes/cytopharynxes and Giardiida ord. nov. for Giardia and Octomitus that lack these, and divide each order into two families. We suggest that this fundamental divergence in manner of feeding and in the symmetry of the cytoskeleton evolved in a free-living diplozoan very early indeed in the evolution of the eukaryotic cell, possibly very soon after the origin of the diplokaryotic state (having two nuclei linked together firmly by the cytoskeleton) and before the evolution of parasitism by distomatids and giardiids, which may have colonized animal guts independently. We discuss the possible relationship between the two archezoan phyla (Metamonada and Microsporidia) and the nature of the first eukaryotic cell in the light of our results and other recent molecular data.

Molecular evolution of the HSP70 multigene family.

Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.

Evidence for multiple xenogenous origins of plastids: comparison of psbA-genes with a xanthophyte sequence

When only plastidic features are considered, it is difficult to distinguish between monophyletic and polyphyletic xenogenous origins of plastids. We suggest that a direct comparison of nuclear and plastidic sequence-similarity pattern will help to solve this problem. The D1 amino acid sequence of six major groups of photosynthetic eukaryotes and of the two groups of photosynthetic prokaryotes are now available, including the psbA-gene product from Bumilleriopsis filiformis, which is the first molecular sequence reported for a xanthophycean alga. Evidence is provided for an independent and polyphyletic origin of plastids from five out of the six major taxa of photosynthetic eukaryotes. This conclusion is reached by comparing a plastid-based pattern of D1 similarity with a nucleus-based similarity pattern published recently. Furthermore, the availability of D1 sequences from five eukaryotic algae led to a re-evaluation of the taxonomic position of Prochlorothrix.

Evolutionary Position of Archaebacteria and Origin of Eukaryotes.

All extant organisms are thought to be classified into three primary kingdoms, eubacteria, eukaryotes, and archaebacteria. Based on the analyses of a pair of duplicated genes, elongation factors EF-Tu/l α and EF-G/2, and catalytic and noncatalytic subunits of ATPase (ATPsynthase), archaebacteria are more closely related to eukaryotes than eubacteria. While this relatedness is certified, phylogenetic relationship among several major groups of archaebacteria (extreme thermophiles, extreme halophiles, and methanogens) and eukaryotes is still unsettled because the phylOgenetic tree topologies among them vary with the genes analysed. The ambiguous situation suggests that archaebacterial major groups and eukaryotes were diverged during very short period in the long course of evolution.

Phylogenetic relationships of the green algeVolvox carteri deduced from small-subunit ribosomal RNA comparisons

The 1788-nucleotide sequence of the small-subunit ribosomal RNA (srRNA) coding region from the chlorophyte Volvox carteri was determined. The secondary structure bears features typical of the universal model of srRNA, including about 40 helices and a division into four domains. Phylogenetic relationships to 17 other eukaryotes, including two other chlorophytes, were explored by comparing srRNA sequences. Similarity values and the inspection of phylogenetic trees derived by distance matrix methods revealed a close relationship between V. carteri and Chlamydomonas reinhardtii. The results are consistent with the view that these Volvocales, and the third green alga, Nanochlorum eucaryotum, are more closely related to higher plants than to any other major eukaryotic group, but constitute a distinct lineage that has long been separated from the line leading to the higher plants.

Organelle origins and ribosomal RNA

As the detailed molecular biology of organelle genomes has unfolded, there has been a general acceptance of the view that plastids and mitochondria are of endosymbiotic, eubacterial origin. Plastid genes are strikingly similar to their eubacterial (particularly cyanobacterial) counterparts in sequence, organization, and mode of expression, and such features strongly support the hypothesis that the plastid and its genome were derived in evolution from a blue-green alga-like endosymbiont. Mitochondria, on the other hand, are problematic: mitochondrial genes are organized and expressed in remarkably diverse ways in the different major groups of eukaryotes, and in no case are these features particularly characteristic of either bacterial or nuclear genomes. There is, however, clear evidence derived from gene sequence supporting the eubacterial ancestry of mitochondria, and some of the most compelling data have come from analyses of mitochondrial ribosomal RNA (rRNA). Plant mitochondrial rRNA genes diverge in sequence at a particularly slow rate, and these genes have proven to be especially supportive of the endosymbiont hypothesis, pointing to an origin of mitochondria from within the alpha subdivision of the purple bacteria. Ribosomal RNA sequences provide a basis for the construction of global phylogenetic trees that probe the evolutionary history of organelles, and that address the question of whether mitochondria and plastids are monophyletic or polyphyletic in origin. Such studies raise the possibility that the rRNA genes of plant mitochondria originated separately from the mitochondrial rRNA genes of other eukaryotes.

THE EUKARYOTIC KINGDOMS.

Abstract- Cladistic analysis of data from ultrastruetural and other cell biological studies indicates that neither the classical two kingdom nor the commonly accepted five kingdom classifications accurately represent the cellular diversity of eukaryotes. The resulting cladogram indicates instead that there are nine major groups of eukaryotes.