Unchanged antigenic properties of a nuclear non-histone protein during phylogenesis

Summary The phyletic distribution of Sm antigen in eukaryotes has been investigated by means of immunochemical techniques. This nuclear antigen, which is an acidic glycoprotein of about 7S with DNA binding ability, is present in all organisms examined. Such evidence suggests a very slow evolutionary rate for at least the antigenic determinant(s) of the Sm antigen.     

Phylogenesis / biotope interactions among formicidae

The development of interspecific recognition and the expression of behavioral plasticity as a function of phyletic distance and the natural environment in which the ants live were investigated.An experimental model involving artificial mixed societies was used in this study. These mixed societies were produced by combining ants from two out of the 11 investigated species. The possibilities thus ranged from situations in which phylogenetically similar ants that live in the same biotype were combined, to those in which the species differ significantly in terms both of phyletic distance and of biotope.The interspecific groups were established in a neutral environment with adult ants less than 24 hours old. The results concerned agonistic and non-agonistic behaviors during the first 15 days. Both the frequency and types of interaction were shown to vary according to the type of group. Two species that share a common habitat are less aggressive and display more non-agonistic behavior than when the species come from different habitats. On the other hand, although aggressive behaviors increase with greater phyletic distance between the species, non-agonistic interactions remain constant.As a general rule, interactions between species from differing environments seem to be determined by the phyletic distance, whereas those between species from the same biotope are controlled by interspecific competition. There is a gradual change in these interactions dependent on the duration of the mixed association.     

Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes.

A semi-explicit arrangement of the lower eukaryotes is provided to serve as a basis for phyletic discussions. No single character is used to determine the position of all the groups. The tree provides no ready separation of protozoa, algae and fungi, groups assigned to these traditional assemblages being considered to be for the most part inextricably interwoven. Photosynthetic forms, whose relationships seem to be more readily discernable, are considered to have given rise repeatedly to nonphotosynthetic forms. The assumption that there are primitive "preflagellar" eukaryotes (red algae, non-flagellated fungi) is adopted. The potential value of mitochondrial features as indicators of broad affinities is emphasised, particularly in determining the probable affinities of non-photosynthetic forms, and this criterion is contra-indicative of a ciliate ancestry for the Metazoa. In the arrangement provided the distributions of chloroplast, mitochondrial and flagellar features match one another well, suggesting their probable co-evolution.     

SHORT NOTES

Bock, W. 2000. Heuristics in systematics. Ostrich 71 (1 &; 2): 41–44.

Avian systematics is not only part of the science of ornithology, but serves heuristically as a foundation for many other analyses in ornithology. Systematics can be divided roughly into two major areas, namely species-level analyses and supraspecific classification. Of greatest significance is the distinction between provisional classifications and standard sequences, the latter are based on widely accepted classifications and have major useful functions such as the arrangement of taxa in handbooks, check-lists, and museum collections. The species concept is part of evolutionary theory, not systematics, and applies to contemporaneous groups of individual organisms. Clear distinctions separate the species concept, the species category, the species taxon, and the phyletic lineage—all usually designated as the “species”. The frequent practice of recognising all distinctive allopatric forms as separate species taxa results in two discrete classes of species taxa which largely destroys their usefulness for other biological analyses, including conservation efforts.     

Organisms can essentially be classified according to two codon patterns

We recently classified 23 bacteria into two types based on their complete genomes; “S-type” as represented by Staphylococcus aureus and “E-type” as represented by Escherichia coli. Classification was characterized by concentrations of Arg, Ala or Lys in the amino acid composition calculated from the complete genome. Based on these previous classifications, not only prokaryotic but also eukaryotic genome structures were investigated by amino acid compositions and nucleotide contents. Organisms consisting of 112 bacteria, 15 archaea and 18 eukaryotes were classified into two major groups by cluster analysis using GC contents at the three codon positions calculated from complete genomes. The 145 organisms were classified into “AT-type” and “GC-type” represented by high A or T (low G or C) and high G or C (low A or T) contents, respectively, at every third codon position. Reciprocal changes between G or C and A or T contents at the third codon position occurred almost synchronously in every codon among the organisms. Correlations between amino acid concentrations (Ala, Ile and Lys) and the nucleotide contents at the codon position were obtained in both “AT-type” and “GC-type” organisms, but with different regression coefficients. In certain correlations of amino acid concentrations with GC contents, eukaryotes, archaea and bacteria showed different behaviors; thus these kingdoms evolved differently. All organisms are basically classifiable into two groups having characteristic codon patterns; organisms with low GC and high AT contents at the third codon position and their derivatives, and organisms with an inverse relationship.     

Perspectives in PDK1 evolution: Insights from photosynthetic and non-photosynthetic organisms

Protein kinases belonging to the AGC group modulate many diverse cellular processes in all eukaryotes. One important way to regulate AGC kinases is through phosphorylation by the upstream kinase PDK1. PDK1 localization and activity usually depend on interactions with phospholipids, which are mediated by a conserved lipid-binding pleckstrin homology (PH) domain. We recently analyzed putative PDK1 sequences from 17 photosynthetic organisms, finding that PDK1s from vascular and nonvascular species seem to be distinguished by the presence or absence of a PH domain, respectively. The only other reported PDK1 lacking a PH domain is from yeast (Saccharomyces cerevisiae). These observations raise questions about how plant PDK1s and their lipid-binding capabilities have evolved in relation to other eukaryotes, and what this means for PDK1 function. Here we use 100 PDK1 sequences from diverse organisms to discuss possible evolutionary aspects of plant PDK1 structure and lipid binding.     

Explanations in evolutionary theory1

The theory of biological evolution is defined in many ways, leading to considerable confusion in its application and testing against objective empirical observations. Evolutionary change is usually defined as genetic which would exclude both cultural and template evolution; hence the qualifying adjective genetic should not be included in the definition of biological evolution. Darwin's theory, always described by him in the singular, is actually a bundle of five independent theories about evolution as advocated by Mayr. Furthermore only one of these theories, that of common descent, is historical, and the other four – evolution as such, gradualism, processes of phyletic evolution and of speciation, and causes of evolution – are nomological. Hence not all evolutionary theory is historical. Biological comparisons can be divided into horizontal and vertical ones and valid conclusions from one type of comparisons cannot be automatically extrapolated to the other. All phyletic evolutionary change, no matter how extensive it may be, never crosses species taxa boundaries; hence it is not possible to distinguish ‘trans‐specific evolution’ (= evolution beyond or above the level of the species) from evolution within the species level. Macroevolution does not differ from microevolution except in the scale of the overall change; no special causes or processes of macroevolution exist.     

The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content

Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than -proteobacteria), and -proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into -proteobacteria as the origin of eukaryotes.     

Characterisation of a Leishmania mexicana knockout lacking guanosine diphosphate-mannose pyrophosphorylase

In eukaryotes, the enzyme GDP-mannose pyrophosphorylase (GDP-MP) is essential for the formation of GDP-mannose, the donor of activated mannose for all glycosylation reactions. Unlike other eukaryotes, where deletion of GDP-mannose pyrophosphorylase is lethal, deletion of this gene in Leishmania mexicana has no effect on viability, but leads to the generation of avirulent parasites. In this study, we show that the null mutants have a perturbed morphology and cytokinesis, retarded growth and increased adherence to the substratum where they form large colonies. The null mutants attach avidly to mouse macrophages, but unlike the wild type organisms, they do not bind to the complement receptor 3 and are slow to induce phagocytosis. Once internalised, they localise to the phagolysosome, but in contrast to wild type organisms which transform into the intracellular amastigote and establish in the macrophage, they are cleared by 24 h in culture and by 5 h in vivo. The null mutants are hypersensitive to human but not mouse complement and to temperature and acidic pH. Surprisingly, in view of the lack of several known host-protective antigens, injection of the mutant parasites into BALB/c mice confers significant and long lasting protection against infection, suggesting that these temperature sensitive mutants are an attractive candidate for a live attenuated vaccine.     

The C. elegans PRMT-3 possesses a type III protein arginine methyltransferase activity

Protein arginine methylation is a common post-translational modification in eukaryotes that is catalyzed by a family of the protein arginine methyltransferases (PRMTs). PRMTs are classified into three types: type I and type II add asymmetrically and symmetrically dimethyl groups to arginine, respectively, while type III adds solely monomethyl group to arginine. However, although the enzymatic activity of type I and type II PRMTs have been reported, the substrate specificity and the methylation activity of type III PRMTs still remains unknown. Here, we report the characterization of Caenorhabditis elegans PRMT-2 and PRMT-3, both of which are highly homologous to human PRMT7. We find that these two PRMTs can bind to S-adenosyl methionine (SAM), but only PRMT-3 has methyltransferase activity for histone H2A depending on its SAM-binding domain. Importantly, thin-layer chromatographic analysis demonstrates that PRMT-3 catalyzes the formation of monomethylated, but not dimethylated arginine. Our study thus identifies the first type III PRMT in C. elegans and provides a means to elucidate the physiological significance of arginine monomethylation in multicellular organisms.     

Protein targeting into plastids: a key to understanding the symbiogenetic acquisitions of plastids

Recent progress in molecular phylogenetics has proven that photosynthetic eukaryotes acquired plastids via primary and secondary endosymbiosis and has given us information about the origin of each plastid. How a photosynthetic endosymbiont became a plastid in each group is, however, poorly understood, especially for the organisms with secondary plastids. Investigating how a nuclear-encoded plastid protein is targeted into a plastid in each photosynthetic group is one of the most important keys to understanding the evolutionary process of symbiogenetic plastid acquisition and its diversity. For organisms which originated through primary endosymbiosis, protein targeting into plastids has been well studied at the molecular level. For organisms which originated through secondary endosymbiosis, molecular-level studies have just started on the plastid-targeted protein-precursor sequences and the targeting pathways of the precursors. However, little information is available about how the proteins get across the inner two or three envelope membranes in organisms with secondary plastids. A good in vitro protein-import system for isolated plastids and a cell transformation system must be established for each group of photosynthetic eukaryotes in order to understand the mechanisms, the evolutionary processes and the diversity of symbiogenetic plastid acquisitions in photosynthetic eukaryotes.     

The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes

ABC (ATP-binding cassette) transporters play an important role in the communication of various substrates across cell membranes. They are ubiquitous in prokaryotes and eukaryotes, and eukaryotic types (EK-types) are distinguished from prokaryotic types (PK-types) in terms of their genes and domain organizations. The EK-types and PK-types mainly consist of exporters and importers, respectively. Prokaryotes have both the EK-types and the PK-types. The EK-types in prokaryotes are usually called "bacterial multidrug ABC transporters," but they are not well characterized in comparison with the multidrug ABC transporters in eukaryotes. Thus, an exhaustive search of the EK-types among diverse organisms and detailed sequence classification and analysis would elucidate the evolutionary history of EK-types. It would also help shed some light on the fundamental repertoires of the wide variety of substrates through which multidrug ABC transporters in eukaryotes communicate. In this work, we have identified the EK-type ABC transporters in 126 prokaryotes using the profiles of the ATP-binding domain (NBD) of the EK-type ABC transporters from 12 eukaryotes. As a result, 11 clusters were identified from 1,046 EK-types ABC transporters. In particular, two large novel clusters emerged, corresponding to the bacterial multidrug ABC transporters related to the ABCB and ABCC families in eukaryotes, respectively. In the genomic context, most of these genes are located alone or adjacent to genes from the same clusters. Additionally, to detect functional divergences in the NBDs, the Kullback-Leibler divergence was measured among these bacterial multidrug transporters. As a result, several putative functional regions were identified, some corresponding to the predicted secondary structures. We also analyzed a phylogeny of the EK-type ABC transporters in both prokaryotes and eukaryotes, which revealed that the EK-type ABC transporters in prokaryotes have certain repertoires corresponding to the conventional ABC protein groups in eukaryotes. On the basis of these findings, we propose an updated evolutionary hypothesis in which the EK-type ABC transporters in both eukaryotes and prokaryotes consisted of several kinds of ABC transporters in putative ancestor cells before the divergence of eukaryotic and prokaryotic cells.     

EVOLUTION, MORPHOGENESIS, AND RECAPITULATION: AN ESSAY ON METAZOAN EVOLUTION

Abstract— The evolution of the Metazoa has to a very large extent been a matter of creating new ways of transforming living matter into animal bodies. As implied from the classification of the subkingdom this process has involved the origin of mechanisms for the construction of a number of phyletic body plans, which in turn have been modified in various ways corresponding to the subordinate taxa within the respective phyla. The ontogenetic development of the metazoans may be subdivided into separate phases, the number of which may vary from one phylum to another, but a typical subdivision comprises five phases: cleavage, form creation, differential growth, allometric growth, and degeneration. Cleavage may be considered as a preparatory phase, whereas true morphogenesis begins with gastrulation. At this stage the phyletic body plan is laid down, in some cases even including features which distinguish some of the higher subordinate taxa—classes and orders—to which the animal belongs. During the phase of differential growth this basic body plan is further modified to correspond to the form characterizing the lower taxa: orders, families, genera, and often even the species. The transformation between differential and allometric growth usually coincides with hatching or birth. Sometimes the specific features develop only during the phase of allometric growth, and under any circumstances the typical morphological differences between young and adult forms are established at this time. Allometric growth usually comes to an end at maturation. The present interpretation is in complete accord with that proposed by von Baer 150 years ago; within each phylum ontogeny occurs in a way corresponding to a recapitulation of the course of phylogenetic evolution. No kind of recapitulation may be observed relating to the evolution between the individual phyla. “as regards its type every organic form becomes by the mode of its formation that which it eventually is. The scheme of development is nothing but the becoming type, and the type the result of the scheme of formation. For that reason the type can be wholly understood only through its mode of development”—K. E. von Baer (1828:258)     

Evolution of proton pumping ATPases: Rooting the tree of life

Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.     

A systematic screen to discover and analyze apicoplast proteins identifies a conserved and essential protein import factor

Parasites of the phylum Apicomplexa cause diseases that impact global health and economy. These unicellular eukaryotes possess a relict plastid, the apicoplast, which is an essential organelle and a validated drug target. However, much of its biology remains poorly understood, in particular its elaborate compartmentalization: four membranes defining four different spaces. Only a small number of organellar proteins have been identified in particular few proteins are known for non-luminal apicoplast compartments. We hypothesized that enlarging the catalogue of apicoplast proteins will contribute toward identifying new organellar functions and expand the realm of targets beyond a limited set of characterized pathways. We developed a bioinformatic screen based on mRNA abundance over the cell cycle and on phyletic distribution. We experimentally assessed 57 genes, and of 30 successful epitope tagged candidates eleven novel apicoplast proteins were identified. Of those, seven appear to target to the lumen of the organelle, and four localize to peripheral compartments. To address their function we then developed a robust system for the construction of conditional mutants via a promoter replacement strategy. We confirm the feasibility of this system by establishing conditional mutants for two selected genes--a luminal and a peripheral apicoplast protein. The latter is particularly intriguing as it encodes a hypothetical protein that is conserved in and unique to Apicomplexan parasites and other related organisms that maintain a red algal endosymbiont. Our studies suggest that this peripheral plastid protein, PPP1, is likely localized to the periplastid compartment. Conditional disruption of PPP1 demonstrated that it is essential for parasite survival. Phenotypic analysis of this mutant is consistent with a role of the PPP1 protein in apicoplast biogenesis, specifically in import of nuclear-encoded proteins into the organelle.     

Regulatory factors for the assembly of thylakoid membrane protein complexes

Major multi-protein photosynthetic complexes, located in thylakoid membranes, are responsible for the capture of light and its conversion into chemical energy in oxygenic photosynthetic organisms. Although the structures and functions of these photosynthetic complexes have been explored, the molecular mechanisms underlying their assembly remain elusive. In this review, we summarize current knowledge of the regulatory components involved in the assembly of thylakoid membrane protein complexes in photosynthetic organisms. Many of the known regulatory factors are conserved between prokaryotes and eukaryotes, whereas others appear to be newly evolved or to have expanded predominantly in eukaryotes. Their specific features and fundamental differences in cyanobacteria, green algae and land plants are discussed.     

Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania

Genomic stability and maintenance of the correct chromosome number are assumed to be essential for normal development in eukaryotes. Aneuploidy is usually associated with severe abnormalities and decrease of cell fitness, but some organisms appear to rely on aneuploidy for rapid adaptation to changing environments. This phenomenon is mostly described in pathogenic fungi and cancer cells. However, recent genome studies highlight the importance of Leishmania as a new model for studies on aneuploidy. Several reports revealed extensive variation in chromosome copy number, indicating that aneuploidy is a constitutive feature of this protozoan parasite genus. Aneuploidy appears to be beneficial in organisms that are primarily asexual, unicellular, and that undergo sporadic epidemic expansions, including common pathogens as well as cancer.