The Mitochondrial Genome of Protists

The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.     

Diverse eukaryotes have retained mitochondrial homologues of the bacterial division protein FtsZ

Mitochondrial fission requires the division of both the inner and outer mitochondrial membranes. Dynamin-related proteins operate in division of the outer membrane of probably all mitochondria, and also that of chloroplasts--organelles that have a bacterial origin like mitochondria. How the inner mitochondrial membrane divides is less well established. Homologues of the major bacterial division protein, FtsZ, are known to reside inside mitochondria of the chromophyte alga Mallomonas, a red alga, and the slime mould Dictyostelium discoideum, where these proteins are likely to act in division of the organelle. Mitochondrial FtsZ is, however, absent from the genomes of higher eukaryotes (animals, fungi, and plants), even though FtsZs are known to be essential for the division of probably all chloroplasts. To begin to understand why higher eukaryotes have lost mitochondrial FtsZ, we have sampled various diverse protists to determine which groups have retained the gene. Database searches and degenerate PCR uncovered genes for likely mitochondrial FtsZs from the glaucocystophyte Cyanophora paradoxa, the oomycete Phytophthora infestans, two haptophyte algae, and two diatoms--one being Thalassiosira pseudonana, the draft genome of which is now available. From Thalassiosira we also identified two chloroplast FtsZs, one of which appears to be undergoing a C-terminal shortening that may be common to many organellar FtsZs. Our data indicate that many protists still employ the FtsZ-based ancestral mitochondrial division mechanism, and that mitochondrial FtsZ has been lost numerous times in the evolution of eukaryotes.     

The mitochondrial genome of protists

The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.     

The phylogeny and evolution of deoxyribonuclease II: an enzyme essential for lysosomal DNA degradation

Deoxyribonuclease II (DNase II) is an endonuclease with optimal activity at low pH, localized within the lysosomes of higher eukaryotes. The origin of this enzyme remains in dispute, and its phylogenetic distribution leaves many questions about its subsequent evolutionary history open. Earlier studies have documented its presence in various metazoans, as well as in Dictyostelium, Trichomonas and, anomalously, a single genus of bacteria (Burkholderia). This study makes use of searches of the genomes of various organisms against known DNase II query sequences, in order to determine the likely point of origin of this enzyme among cellular life forms. Its complete absence from any other bacteria makes prokaryotic origin unlikely. Convincing evidence exists for DNase II homologs in Alveolates such as Paramecium, Heterokonts such as diatoms and water molds, and even tentative matches in green algae. Apparent absences include red algae, plants, fungi, and a number of parasitic organisms. Based on this phylogenetic distribution and hypotheses of eukaryotic relationships, the most probable explanation is that DNase II has been subject to multiple losses. The point of origin is debatable, though its presence in Trichomonas and perhaps in other evolutionarily basal "Excavate" protists such as Reclinomonas, strongly support the hypothesis that DNase II arose as a plesiomorphic trait in eukaryotes. It probably evolved together with phagocytosis, specifically to facilitate DNA degradation and bacteriotrophy. The various absences in many eukaryotic lineages are accounted for by loss of phagotrophic function in intracellular parasites, in obligate autotrophs, and in saprophytes.     

Analysis of dinoflagellate mitochondrial protein sorting signals indicates a highly stable protein targeting system across eukaryotic diversity

Protein targeting into mitochondria from the cytoplasm is fundamental to the cell biology of all eukaryotes. Our understanding of this process is heavily biased towards “model” organisms, such as animals and fungi, and it is less clear how conserved this process is throughout diverse eukaryotes. In this study, we have surveyed mitochondrial protein sorting signals from a representative of the dinoflagellate algae. Dinoflagellates are a phylum belonging to the group Alveolata, which also includes apicomplexan parasites and ciliates. We generated 46 mitochondrial gene sequences from the dinoflagellate Karlodinium micrum and analysed these for mitochondrial sorting signals. Most of the sequences contain predicted N-terminal peptide extensions that conform to mitochondrial targeting peptides from animals and fungi in terms of length, amino acid composition, and propensity to form amphipathic α-helices. The remainder lack predicted mitochondrial targeting peptides and represent carrier proteins of the inner mitochondrial membrane that have internal targeting signals in model eukaryotes. We tested for functional conservation of the dinoflagellate mitochondrial sorting signals by expressing K. micrum mitochondrial proteins in the fungus Saccharomyces cerevisiae. Both the N-terminal and internal targeting signals were sufficiently conserved to operate in this distantly related system. This study indicates that the character of mitochondrial sorting signals was well established prior to the radiation of major eukaryotic lineages and has shown remarkable conservation during long periods of evolution.     

Mitochondrial genome structure of photosynthetic eukaryotes

Current ideas of plant mitochondrial genome organization are presented. Data on the size and structural organization of mtDNA, gene content, and peculiarities are summarized. Special emphasis is given to characteristic features of the mitochondrial genomes of land plants and photosynthetic algae that distinguish them from the mitochondrial genomes of other eukaryotes. The data published before the end of 2014 are reviewed.     

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.     

Genome diversity in microbial eukaryotes

The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.     

Dasyclads, cyclocrinitids and receptaculitids: comparative morphology and paleoecology

The cyclocrinitids are an extinct tribe of dasycladacean green algae. They were anatomically very similar to certain Recent dasyclads, even at early growth stages. The morphology and preservation of cyclocrinitids strongly suggest that they had a siphonous cellular organization with extracellular, aragonitic calcification; these features are characteristic of living dasyclads. The light surficial calcification of cyclocrinitids and other dasyclads had important paleoecological effects. It restricted them to low-energy waters, as it provided relatively little structural support. It also confined them to warm, tropical waters; they are good paleoequatorial indicators. The decline of these algae during the late Ordovician and early Silurian may therefore reflect the simultaneous cooling and glaciation. Receptaculitids are entirely unrelated organisms. Their meroms have several distinctive features; they are not homologous to the lateral branches of cyclocrinitids or dasyclads. Receptaculitid calcification was extensive and their thalli were apparently quite sturdy; they often occurred in reefs. Receptaculitids also lived in high-latitude, cold-water environments. Thus, they were ecologically unlike any calcareous green algae, and cannot be used as paleoequatorial indicators. Receptaculitids remain problematical, although the arrangement of meroms suggests plant affinities. □ Calcareous algae, Problematica, Dasycladales, Cyclocriniteae, Receptaculitales, morphology, classification, paleoecology, paleogeography .     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Evidence for an early evolutionary emergence of γ-type carbonic anhydrases as components of mitochondrial respiratory complex I

Background  

The complexity of mitochondrial complex I (CI; NADH:ubiquinone oxidoreductase) has increased considerably relative to the homologous complex in bacteria. Comparative analyses of CI composition in animals, fungi and land plants/green algae suggest that novel components of mitochondrial CI include a set of 18 proteins common to all eukaryotes and a variable number of lineage-specific subunits. In plants and green algae, several purportedly plant-specific proteins homologous to γ-type carbonic anhydrases (γCA) have been identified as components of CI. However, relatively little is known about CI composition in the unicellular protists, the characterizations of which are essential to our understanding of CI evolution.     

Search for Clues to the Evolutionary Meaning of Ciliate Phylogeny*†

SYNOPSIS. Progress in ciliatology and in allied fields may demystify ciliate phylogenetics. Concentration on hymenostomes (mainly Tetrahymena and Paramecium) may have obscured directional features of ciliate physiology in phylogenetic problems. Therefore, means are suggested for “domesticating” the presumptively primitive, predominantly marine, sand-dwelling gymnostomes having nondividing diploid macronuclei. The prize quarry is the marine psammophile Stephanopogon whose homokaryotic condition may mark it as a living fossil. Eventual axenic cultivation of these “primitive” ciliates may be aided by use as food of easily grown photosynthetic prokaryotes, some isolated from the marine sulfuretum or adjacent aerobic muds and sands where “karyorelictid” ciliates flourish. We assume that: (a) the macronucleus evolved as a coordinator of chemical and physical signals, for efficient detection of food and toxins; (b) oral structures evolved meanwhile as sensors as well as mechanical food-gatherers. This conjunction enabled complexity of adaptive behavior and evolutionary success. Ciliate origins cannot be considered apart from origin(s) of phagotrophy and its underlying versatile heterotrophy. Because of the well developed heterotrophy in some photosynthetic prokaryotes (including several proposed as food organisms), they are viewed as alternatives to blue-green algae as forebears of eukaryotes. Nor can ciliate origins be considered apart from origin(s) of eukaryotes. A check of these assumptions—that Stephanopogon and gymnostomes with nondividing macronuclei are primitive—may be forthcoming from sequencing amino acids in certain key enzymes, given an adequate sampling of ciliates, flagellates (especially dinoflagellates and cryptomonads), lower fungi, and photosynthetic prokaryotes other than blue-green algae.     

Flagellate Phylogeny: A Study in Conflicts*

SYNOPSIS. Information relating to the ultrastructure of 4 organellar systems of flagellates—nuclei (including mitosis), flagella, mitochondria and chloroplasts—is examined for bearing on the probable phylogeny of the principal flagellate groups, first considered singly and then in combination. The mitotic mechanism has not proved to be as conservative a character as might be hoped, but still remains characteristic for the average condition in many of the groups. Flagellar features are useful if allowance is made for the reduction or multiplication of the basic pair, and the loss of lateral and terminal hairs seems to have occurred independently several times. The presence of paraxial rods within flagella may be a useful indication of affinity. Rootlet systems are not dealt with in detail here, although the possible similarity between axial microtubular sheets in axostylar flagellates and some members of the green algae containing “manchettes” is noted. The basic patterns of chloroplast internal structure are summarized and their general agreement with other characters is affirmed, noting however that cryptomonads may be closer to the green flagellates (including euglenoids) than is generally accepted. Attention is drawn to the potential value of internal mitochondrial morphology as an indicator of large assemblages. Finally, a “tree” based on multiple cell organizational features is presented and discussed.     

Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta)

In most eukaryotes the subunit 2 of cytochrome c oxidase (COX2) is encoded in intact mitochondrial genes. Some green algae, however, exhibit split cox2 genes (cox2a and cox2b) encoding two polypeptides (COX2A and COX2B) that form a heterodimeric COX2 subunit. Here, we analyzed the distribution of intact and split cox2 gene sequences in 39 phylogenetically diverse green algae in phylum Chlorophyta obtained from databases (28 sequences from 22 taxa) and from new cox2 data generated in this work (23 sequences from 18 taxa). Our results support previous observations based on a smaller number of taxa, indicating that algae in classes Prasinophyceae, Ulvophyceae, and Trebouxiophyceae contain orthodox, intact mitochondrial cox2 genes. In contrast, all of the algae in Chlorophyceae that we examined exhibited split cox2 genes, and could be separated into two groups: one that has a mitochondrion-localized cox2a gene and a nucleus-localized cox2b gene ("Scenedesmus-like"), and another that has both cox2a and cox2b genes in the nucleus ("Chlamydomonas-like"). The location of the split cox2a and cox2b genes was inferred using five different criteria: differences in amino acid sequences, codon usage (mitochondrial vs. nuclear), codon preference (third position frequencies), presence of nucleotide sequences encoding mitochondrial targeting sequences and presence of spliceosomal introns. Distinct green algae could be grouped according to the form of cox2 gene they contain: intact or fragmented, mitochondrion- or nucleus-localized, and intron-containing or intron-less. We present a model describing the events that led to mitochondrial cox2 gene fragmentation and the independent and sequential migration of cox2a and cox2b genes to the nucleus in chlorophycean green algae. We also suggest that the distribution of the different forms of the cox2 gene provides important insights into the phylogenetic relationships among major groups of Chlorophyceae.     

Organelle fission in eukaryotes

The cellular machineries that power chloroplast and mitochondrial division in eukaryotes carry out the topologically challenging job of constricting and severing these double-membraned organelles. Consistent with their endosymbiotic origins, mitochondria in protists and chloroplasts in photosynthetic eukaryotes have evolved organelle-targeted forms of FtsZ, the prokaryotic ancestor of tubulin, as key components of their fission complexes. In fungi, animals and plants, mitochondria no longer utilize FtsZ for division, but several mitochondrial division proteins that localize to the outer membrane and intermembrane space, including two related to the filament-forming dynamins, have been identified in yeast and animals. Although the reactions that mediate organelle division are not yet understood, recent progress in uncovering the constituents of the organelle division machineries promises rapid advancement in our understanding of the biochemical mechanisms underlying the distinct but related processes of chloroplast and mitochondrial division in eukaryotes.     

绿藻光合生物制氢技术进展

氢能作为可再生、环境友好的能源,已成为营造可持续发展的经济节约型社会的理想能源。绿藻因能利用光能分解水产氢,被称为最有应用前景的方法之一。本文将综述绿藻光合产氢的原理,介绍该生物制氢技术的研究现状和最新进展,并对其发展趋势做以展望。     

Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space

The mitochondrial inner and outer membranes are composed of a variety of integral membrane proteins, assembled into the membranes posttranslationally. The small translocase of the inner mitochondrial membranes (TIMs) are a group of approximately 10 kDa proteins that function as chaperones to ferry the imported proteins across the mitochondrial intermembrane space to the outer and inner membranes. In yeast, there are 5 small TIM proteins: Tim8, Tim9, Tim10, Tim12, and Tim13, with equivalent proteins reported in humans. Using hidden Markov models, we find that many eukaryotes have proteins equivalent to the Tim8 and Tim13 and the Tim9 and Tim10 subunits. Some eukaryotes provide "snapshots" of evolution, with a single protein showing the features of both Tim8 and Tim13, suggesting that a single progenitor gene has given rise to each of the small TIMs through duplication and modification. We show that no "Tim12" family of proteins exist, but rather that variant forms of the cognate small TIMs have been recently duplicated and modified to provide new functions: the yeast Tim12 is a modified form of Tim10, whereas in humans and some protists variant forms of Tim9, Tim8, and Tim13 are found instead. Sequence motif analysis reveals acidic residues conserved in the Tim10 substrate-binding tentacles, whereas more hydrophobic residues are found in the equivalent substrate-binding region of Tim13. The substrate-binding region of Tim10 and Tim13 represent structurally independent domains: when the acidic domain from Tim10 is attached to Tim13, the Tim8-Tim13(10) complex becomes essential and the Tim9-Tim10 complex becomes dispensable. The conserved features in the Tim10 and Tim13 subunits provide distinct binding surfaces to accommodate the broad range of substrate proteins delivered to the mitochondrial inner and outer membranes.     

Animals (Animalia) in the system of organisms. 1. Typological systems

Since times of Aristotle animals were considered as a group, opposing to plants. The last were distinguished by two characters. Plants as distinct from animals live the attached way of a life and all nutrients receive from a substratum on which live and from the surrounding air. Animals live an active way of life and exist due to digestion. Fungi at such definition belong to plants. Only in second half of XX centuries due to works of Whittaker and of Tachtadjan fungi have received the separate status equally with plants and animals. In this new system of a plant embraced either oxygenic phototrophs, or photosynthetic eukaryotes. The traditional characters distinguishing animals from plants and fungi are in detail analysed. Many of them appeared formal, not reflecting the structure of relationship. Comparing heterotrophs some authors saw in absorptive nutrition the main difference of fungi from animals. However on mechanisms of receipt of substances in a cell fungi, animals and plants do not differ. Phagocytosis and pinocytosis (clathrin-mediated endocytosis), considered as the most characteristic feature of animals, are revealed both in fungi, and in plants. On photosynthetic activity plants form heterogeneous group, differing on primary and secondary plastids. The last besides have the various origin connected to symbiogenesis of the host cell with red or green algae. Heterotrophy cannot be considered as a uniting attribute of fungi and animals. It is essentially different and focused on diverse food sources. Evolution of animals is connected to perfection of structure of a plasmatic membrane and saturation by its molecules allowing a cell, and through it all organism to be guided in an environment and adequally to be up to external irritants. At a cellular level animals use the various mechanisms of cellular activity connected to moving of cells, their combination in aggregates and complexes or, on the contrary, separation in new cellular configurations. The complex of cellular adaptations connected to the analysis of external signals and adequate response to them of cells, underlies the phenomenon of irritability. At a cellular level irritability is mediated through work of the actin apparatus. Lamarck in "Philosophie zoologique" considered irritability as the main distinctive feature of animals. Evolution of plants and fungi went in a direction of development of a secondary metabolism. The secondary metabolism, concerning synthesis of protective substances, is peculiar to all sedentary organisms, including the animals.