Early Eukaryotes Research Articles

New physiological functions for drug-transporting P-glycoproteins?

New physiological functions for drug-transporting P-glycoproteins?

Evolution of the protists and protistan parasites from the perspective of molecular systematics

Unlike prokaryotes, the Protista are rich in morphological and ultrastructure information. Their amazing phenotypic diversity permits assignment of many protists to cohesive phyletic assemblages but sometimes blurs relationships between major lineages. With the advent of molecular techniques, it became possible to test evolutionary hypotheses that were originally formulated according to shared phenotypic traits. More than any other gene family, studies of rRNAs changed our understanding of protist evolution. Stramenopiles (oomycetes, chrysophytes, phaeophytes, synurophytes, diatoms, xanthophytes, bicosoecids, slime nets) and alveolates (dinoflagellates, apicomplexans, ciliates) are two novel, complex evolutionary assemblages which diverged nearly simultaneously with animals, fungi, plants, rhodophytes, haptophytes and a myriad of independent amoeboid lineages. Their separation may have occurred one billion years ago and collectively these lineages make up the “crown” of the eukaryotic tree. Deeper branches in the eukaryotic tree show 16S-like rRNA sequence variation that is much greater than that observed within the Archaea and the Bacteria. A progression of independent protist branches, some as ancient as the divergence between the two prokaryotic domains, preceded the sudden radiation of “crown” groups. Trichomonads, diplomonads and Microsporidia are basal to all other eukaryotes included in rRNA studies. Together with pelobionts, oxymonads, retortamonads and hypermastigids, these amitochondriate taxa comprise the Archaezoa. This skeletal phylogeny suggested that early branching eukaryotes lacked mitochondria, peroxisomes and typical stacked Golgi dictyosomes. However, recent studies of heat shock proteins indicate that the first eukaryotes may have had mitochondria. When evaluated in terms of evolution of ultrastructure, lifestyles and other phenotypic traits, the rRNA phylogenies provide the most consistent of molecular trees. They permit identification of the phylogenetic affinity of many parasitic groups as well as a means to integrate molecular and cell biological information from diverse eukaryotes. We must place greater emphasis upon improved phylogenetic inference techniques and investigations of genomic diversity in protists.

Early origin of foraminifera suggested by SSU rRNA gene sequences.

Foraminifera are one of the largest groups of unicellular eukaryotes with probably the best known fossil record. However, the origin of foraminifera and their phylogenetic relationships with other eukaryotes are not well established. In particular, two recent reports, based on ribosomal RNA gene sequences, have reached strikingly different conclusions about foraminifera's evolutionary position within eukaryotes. Here, we present the complete small subunit (SSU) rRNA gene sequences of three species of foraminifera. Phylogenetic analysis of these sequences indicates that they branch very deeply in the eukaryotic evolutionary tree: later than those of the amitochondrial Archezoa, but earlier than those of the Euglenozoa and other mitochondria-bearing phyla. Foraminifera are clearly among the earliest eukaryotes with mitochondria, but because of the peculiar nature of their SSU genes we cannot be certain that they diverged first, as our data suggest.

Are red algae plants?

For 200 years prior to the 1938 publication of H. F. Copeland, all authorities (with one exception) classified red algae (Rhodophyta.) within Kingdom Plantae or its equivalent. Copeland's reclassification of red algae within Kingdom Protista or Protoctista drew from an alternative tradition, dating to Cohn in 1867, in which red algae were viewed as the earliest or simplest eukaryotes. Analyses of ribosomal RNA (rRNA) sequence data initially favoured Copeland's reclassification. Many more rRNA gene (rDNA) sequences are now available from the eukaryote lineages most closely related to red algae, and based on these data, the hypothesis that red algae and green plants are sister groups cannot be rejected. An increasing body of sequence, intron-location and functional data from nuclearand mitochondrially encoded proteins likewise supports a sister-group relationship between red algae and green plants. Submerging Kingdoms Plantae, Animalia and Fungi into Eukarya would provide a more natural framework for the eventual resolution of whether red algae are plants or protists.

Hypothesis for the evolution of three-helix Chl a/b and Chl a/c light-harvesting antenna proteins from two-helix and four-helix ancestors

The nuclear-encoded Chl a/b and Chl a/c antenna proteins of photosynthetic eukaryotes are part of an extended family of proteins that also includes the early light-induced proteins (ELIPs) and the 22 kDa intrinsic protein of PS II (encoded by psbS gene). All members of this family have three transmembrane helices except for the psbS protein, which has four. The amino acid sequences of these proteins are compared and related to the three-dimensional structure of pea LHC II Type I (Kühlbrandt and Wang, Nature 350: 130-134, 1991). The similarity of psbS to the three-helix members of the family suggests that the latter arose from a four-helix ancestor that lost its C-terminal helix by deletion. Strong internal similarity between the two halves of the psbS protein suggests that it in turn arose as the result of the duplication of a gene encoding a two-helix protein. Since psbS is reported to be present in at least one cyanobacterium, the ancestral four-helix protein may have been present prior to the endosymbiotic event or events that gave rise to the photosynthetic eukaryotes. The Chl a/b and Chl a/c antenna proteins, and the immunologically-related proteins in the rhodophytes may have had a common ancestor which was present in the early photosynthetic eukaryotes, and predated their division into rhodophyte, chromophyte and chlorophyte lineages. The LHC I-LHC II divergence probably occurred before the separation of higher plants from chlorophyte algae and euglenophytes, and the different Types of LHC I and LHC II proteins arose prior to the separation of angiosperms and gymnosperms.

Identification of protein phosphatase inhibitors of the microcystin class in the marine environment

Toxins produced by marine phytoplankton represent a severe global health hazard to humans that eat seafood and are also responsible for massive natural fish kills in specialized bloom situations. Tumour-promoting hepatotoxins from the freshwater microcystin/nodularin class were identified in Northeastern Pacific Ocean, Eastern Canadian and European mussels for the first time. These hepatotoxins were detected at biologically active levels up to three-fold higher than accepted quarantine levels for the diarrhetic shellfish toxin okadaic acid (OA), based on their activity (in microcystin-LR equivalent units) in a liquid chromatography (LC)-linked protein phosphatase bioassay. The presence of microcystins/nodularins in oceanic shellfish identifies a potentially novel class of intoxication which is also prevalent in other forms of marine aquatic life, namely sponges and fish. The widespread presence of prokaryotic microcystins and nodularins in the marine environment may be indicative of the importance of signal transduction pathways involving potent inhibition of protein phosphatases in early marine eukaryotes.

Precambrian oxygen levels estimated from the biochemistry and physiology of early eukaryotes

Recent work on the biochemistry of living organisms has shown that the organelles which eukaryotic cells use for photosynthesis and aerobic respiration are of bacterial origin, and that they were imported by eubacterial endosymbionts some time after the existence of the last common ancestor of all modern eukaryotes. However, all living eukaryotes need a certain amount of molecular oxygen for the biosynthesis of vital compounds such as the sterols that are used to stiffen cell membranes. It follows that some dissolved oxygen must have been available to the ancestral “anaerobic” eukaryotes before they acquired their organelles. A minimum age for the first occurrence of such organisms is given by the discovery of modified sterols (steranes) in organic-rich sedimentary rocks about 1.7 Ga old from the McArthur Basin of northern Australia. Fully organelled eukaryotes need even more oxygen if they are to use their mitochondria for aerobic respiration. Some of the oldest fossils that are likely to be the remains of photosynthetic eukaryotes are also from the McArthur Basin. If these sizeable, unicellular algae had functional mitochondria as well as chloroplasts, the oxygen concentration of surface waters some 1.6–1.8 Ga ago is unlikely to have been less than that required for aerobic respiration (> - 0.01 PAL). The oldest convincing megascopic eukaryote, Grypania spiralis, is found ∼1.4 Ga-old strata in China, India, and the U.S.A. Grypania was a corkscrew-shaped “alga” up to 2 mm in diameter and 0.6 m in length which seems to have lived attached to the sea floor. Unless Grypania used oxygen produced by its own chloroplasts, it should have needed between a hundredth and tenth of the present atmospheric level of oxygen (0.01–0.1 PAL O 2) to survive. A similar atmospheric oxygen concentration may have been more than enough to sustain the sheet-like animals of the Ediacara fauna. However, it is possible that their extraordinary geometry was an adaptation to low oxygen levels (≤ 0.01 PAL O 2) which may have persisted until the end of the Precambrian. Unfortunately, these estimates of the minimal oxygen requirements of known Precambrian eukaryotes do little at this stage to constrain models for the growth of atmospheric oxygen during the Proterozoic. It is therefore unknown whether oxygen levels remained relatively low (< 0.1 PAL) until near the end of the Precambrian or climbed rapidly to near modern values after oceanic oxygen sinks were exhausted some 2 Ga ago.

Precambrian oxygen levels estimated from the biochemistry and physiology of early eukaryotes

Recent work on the biochemistry of living organisms has shown that the organelles which eukaryotic cells use for photosynthesis and aerobic respiration are of bacterial origin, and that they were imported by eubacterial endosymbionts some time after the existence of the last common ancestor of all modern eukaryotes. However, all living eukaryotes need a certain amount of molecular oxygen for the biosynthesis of vital compounds such as the sterols that are used to stiffen cell membranes. It follows that some dissolved oxygen must have been available to the ancestral “anaerobic” eukaryotes before they acquired their organelles. A minimum age for the first occurrence of such organisms is given by the discovery of modified sterols (steranes) in organic-rich sedimentary rocks about 1.7 Ga old from the McArthur Basin of northern Australia. Fully organelled eukaryotes need even more oxygen if they are to use their mitochondria for aerobic respiration. Some of the oldest fossils that are likely to be the remains of photosynthetic eukaryotes are also from the McArthur Basin. If these sizeable, unicellular algae had functional mitochondria as well as chloroplasts, the oxygen concentration of surface waters some 1.6–1.8 Ga ago is unlikely to have been less than that required for aerobic respiration (> - 0.01 PAL). The oldest convincing megascopic eukaryote, Grypania spiralis, is found ∼1.4 Ga-old strata in China, India, and the U.S.A. Grypania was a corkscrew-shaped “alga” up to 2 mm in diameter and 0.6 m in length which seems to have lived attached to the sea floor. Unless Grypania used oxygen produced by its own chloroplasts, it should have needed between a hundredth and tenth of the present atmospheric level of oxygen (0.01–0.1 PAL O 2) to survive. A similar atmospheric oxygen concentration may have been more than enough to sustain the sheet-like animals of the Ediacara fauna. However, it is possible that their extraordinary geometry was an adaptation to low oxygen levels (≤ 0.01 PAL O 2) which may have persisted until the end of the Precambrian. Unfortunately, these estimates of the minimal oxygen requirements of known Precambrian eukaryotes do little at this stage to constrain models for the growth of atmospheric oxygen during the Proterozoic. It is therefore unknown whether oxygen levels remained relatively low (< 0.1 PAL) until near the end of the Precambrian or climbed rapidly to near modern values after oceanic oxygen sinks were exhausted some 2 Ga ago.

Proposed role of drug-metabolizing enzymes: regulation of steady state levels of the ligands that effect growth, homeostasis, differentiation, and neuroendocrine functions.

Every ligand known to bind to a receptor in the nuclear hormone receptor superfamily is involved in a variety of signal transduction pathways effecting growth, morphogenesis, homeostasis, proliferation, and neuroendocrine functions. Often these ligands are associated with increases in particular subsets of cytochromes P450 and other drug-metabolizing enzymes. Interestingly, certain of these enzymes participate in the metabolism (synthesis as well as degradation) of these ligands. It appears that genes coding for certain drug-metabolizing enzymes might have existed on this planet at least 1 billion years before the presence of plants, animals, and drugs. An early role for oxidative enzymes in prokaryotes most likely involved energy substrate utilization: insertion of oxygen into various inaccessible carbon and other food sources, thereby rendering them accessible to further metabolism. It is proposed that a later development of these "drug-metabolizing enzymes" in prokaryotes and early eukaryotes might be related to their metabolic ability to control the steady state levels of the ligands that modulate cell division, growth, morphogenesis, and mating, and that this role has diversified in numerous additional signal transduction pathways and exists today in all eukaryotes.

Primary and secondary structure of dinoflagellate U5 small nuclear RNA.

U5 RNA is one of the six capped small nuclear RNAs present in most eukaryotic cells. Like U1, U2, U4 and U6 RNAs, U5 RNA is associated with hnRNP particles and is thus probably involved in some, as yet undefined, aspects of pre-messenger RNA processing. In this study, the complete nucleotide sequence of U5 RNA of a dinoflagellate, Crypthecodinium cohnii was determined. The analysis of this dinoflagellate U5 RNA sequence showed that a) the sequence homology between human, rat and chicken U5 RNA sequences and dinoflagellate U5 RNA sequence is 64%; b) the extent and the position of post-transcriptional modifications are similar to those found in U5 RNA of higher eukaryotes; c) although the dinoflagellate U5 RNA is shorter in length (108 nucleotides long vs 117 long in human, rat and chicken cells), the RNA fits well into the same secondary structure proposed for U5 RNA of higher eukaryotes (Krol et al. (1981) Nucl. Acids Res. 9, 769); and d) the AUn nucleotide sequence protected by the Sm-antigen and the tight secondary structure found near the 3'-end of other U-RNAs was also found in dinoflagellate U5 RNA. The high order of homology observed between dinoflagellate U5 RNA and U5 RNA of higher eukaryotes indicates that dinoflagellates are more closely related to metazoans than to early eukaryotes.

Devonian and modern relatives of the Precambrian Eosphaera: possible significance for the early eukaryotes

The Middle Precambrian problematical microorganism Eosphaera Barghoorn and Eosphaera-like structures known from Early and Middle Precambrian banded iron formations have been compared with the recently discovered Devonian volvocacean alga Eovolvox Kaźmierczak and some modern colonial Volvocales. The volvocacean interpretation of Eosphaera implies that algal eukaryotes (green phytoflagellates) werc already prewmt in the earth biosphere before at least 1.9 b. y. ago (Gunflint Iron Formaticn), and probably before 2.7 b. y. ago (Soudan Iron Formation). The type of metabolism and thc oxygen requirements of modern colonial Volvocales indicate that Eosphaera was most probably a photoorgano-trophic (mixotrophic) organism able to live in the extremely oxygen-deficicnt or anoxy-genous Early Precambrian environment. As an oxygen-releasing photosynthesizer, Eosphaera could have played a considerable role in the production of free oxygen during the Precambrian. The abundance of Eospkaera-like ferriferous structures in the iron microbands of many banded iron formations implies active participation of these organisns in the formation of Precambrian sedimentary iron ores. The exclusively fresh-water habitat of extant volvocacean algae suggests that the Procambrian environments inhabited by Eosphaera were non-marine.