Three puzzles in hierarchical evolution

The maximum degree of hierarchical structure of organisms hasrisen over the history of life, notably in three transitions:the origin of the eukaryotic cell from symbiotic associationsof prokaryotes; the emergence of the first multicellular individualsfrom clones of eukaryotic cells; and the origin of the firstindividuated colonies from associations of multicellular organisms.The trend is obvious in the fossil record, but documenting itusing a high-resolution hierarchy scale reveals three puzzles:1) the rate of origin of new levels accelerates, at least untilthe early Phanerozoic; 2) after that, the trend may slow oreven stop; and 3) levels may sometimes arise out of order. Thethree puzzles and their implications are discussed; a possibleexplanation is offered for the first.     

Spatial separation of ribosomes and DNA in Asgard archaeal cells

The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1–2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50–280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.Subject terms: Soil microbiology, Microbial ecology, Archaeal physiology     

Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection

Two central biophysical laws describe sensory responses to input signals. One is a logarithmic relationship between input and output, and the other is a power law relationship. These laws are sometimes called the Weber-Fechner law and the Stevens power law, respectively. The two laws are found in a wide variety of human sensory systems including hearing, vision, taste, and weight perception; they also occur in the responses of cells to stimuli. However the mechanistic origin of these laws is not fully understood. To address this, we consider a class of biological circuits exhibiting a property called fold-change detection (FCD). In these circuits the response dynamics depend only on the relative change in input signal and not its absolute level, a property which applies to many physiological and cellular sensory systems. We show analytically that by changing a single parameter in the FCD circuits, both logarithmic and power-law relationships emerge; these laws are modified versions of the Weber-Fechner and Stevens laws. The parameter that determines which law is found is the steepness (effective Hill coefficient) of the effect of the internal variable on the output. This finding applies to major circuit architectures found in biological systems, including the incoherent feed-forward loop and nonlinear integral feedback loops. Therefore, if one measures the response to different fold changes in input signal and observes a logarithmic or power law, the present theory can be used to rule out certain FCD mechanisms, and to predict their cooperativity parameter. We demonstrate this approach using data from eukaryotic chemotaxis signaling.     

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.     

A statistical anomaly indicates symbiotic origins of eukaryotic membranes

Compositional analyses of nucleic acids and proteins have shed light on possible origins of living cells. In this work, rigorous compositional analyses of ∼5000 plasma membrane lipid constituents of 273 species in the three life domains (archaea, eubacteria, and eukaryotes) revealed a remarkable statistical paradox, indicating symbiotic origins of eukaryotic cells involving eubacteria. For lipids common to plasma membranes of the three domains, the number of carbon atoms in eubacteria was found to be similar to that in eukaryotes. However, mutually exclusive subsets of same data show exactly the opposite—the number of carbon atoms in lipids of eukaryotes was higher than in eubacteria. This statistical paradox, called Simpson''s paradox, was absent for lipids in archaea and for lipids not common to plasma membranes of the three domains. This indicates the presence of interaction(s) and/or association(s) in lipids forming plasma membranes of eubacteria and eukaryotes but not for those in archaea. Further inspection of membrane lipid structures affecting physicochemical properties of plasma membranes provides the first evidence (to our knowledge) on the symbiotic origins of eukaryotic cells based on the “third front” (i.e., lipids) in addition to the growing compositional data from nucleic acids and proteins.     

The origin of the eukaryotic cell. III. Principles of the morphofunctional organization of the eukaryotic cell

The eukaryotic plasmalemma, eukaryotic cytoplasm with its usual cytomembranes, and eukaryotic nucleus are obligatory components of the eukaryotic cell. All other structural elements (organelles) are only derivates of the aforesaid cell components and they may be absent sometimes. There are protozoans having simultaneously no flagelles, mitochondria and chloroplasts (all the representatives of phylum Microspora, amoeba Pelomyxa palustris, and others). The following five general principles play the main role in the morphofunctional organization of the cell. The principle of hierarchy of block organization of living systems. Complex morphofunctional blocks (organelles) specific for the eukaryotic cell are formed. The compartmentalization principle. The main cell organelles (nuclei, flagellae, mitochondria, chloroplasts, etc.) undergo a relative morphological isolation from each other and other cell organelles by means of the total or partial surrounding by membranes; this may ensure the originality of their evolution and function. The principle of poly- and oligomerization of morphofunctional blocks. It permits the cell to enlarge its sizes and to raise the level of integration. The principle of heterochrony, including three subprinciples: conservatism of useful signs; a strong acceleration of evolutionary development of the separate blocks; simplification of the structure, reduction or total disappearance of some blocks. It explains a preservation of prokaryotic signs in the eukaryotic cell or in its organelles. The principle of independent origin of similar morphofunctional blocks in the process of evolution of living systems. The parallelism of the signs in unrelated groups of cells (or protists) arises due to this principle.     

Porphyromonas gingivalis as a Model Organism for Assessing Interaction of Anaerobic Bacteria with Host Cells

Anaerobic bacteria far outnumber aerobes in many human niches such as the gut, mouth, and vagina. Furthermore, anaerobic infections are common and frequently of indigenous origin. The ability of some anaerobic pathogens to invade human cells gives them adaptive measures to escape innate immunity as well as to modulate host cell behavior. However, ensuring that the anaerobic bacteria are live during experimental investigation of the events may pose challenges. Porphyromonas gingivalis, a Gram-negative anaerobe, is capable of invading a variety of eukaryotic non-phagocytic cells. This article outlines how to successfully culture and assess the ability of P. gingivalis to invade human umbilical vein endothelial cells (HUVECs). Two protocols were developed: one to measure bacteria that can successfully invade and survive within the host, and the other to visualize bacteria interacting with host cells. These techniques necessitate the use of an anaerobic chamber to supply P. gingivalis with an anaerobic environment for optimal growth.The first protocol is based on the antibiotic protection assay, which is largely used to study the invasion of host cells by bacteria. However, the antibiotic protection assay is limited; only intracellular bacteria that are culturable following antibiotic treatment and host cell lysis are measured. To assess all bacteria interacting with host cells, both live and dead, we developed a protocol that uses fluorescent microscopy to examine host-pathogen interaction. Bacteria are fluorescently labeled with 2'',7''-Bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein acetoxymethyl ester (BCECF-AM) and used to infect eukaryotic cells under anaerobic conditions. Following fixing with paraformaldehyde and permeabilization with 0.2% Triton X-100, host cells are labeled with TRITC phalloidin and DAPI to label the cell cytoskeleton and nucleus, respectively. Multiple images taken at different focal points (Z-stack) are obtained for temporal-spatial visualization of bacteria. Methods used in this study can be applied to any cultivable anaerobe and any eukaryotic cell type.     

Mosaic origin of the mitochondrial proteome

Although the origin of mitochondria from the endosymbiosis of an α-proteobacterium is well established, the nature of the host cell, the metabolic complexity of the endosymbiont and the subsequent evolution of the proto-mitochondrion into all its current appearances are still the subject of discovery and sometimes debate. Here we review what has been inferred about the original composition and subsequent evolution of the mitochondrial proteome and essential mitochondrial systems. The evolutionary mosaic that currently constitutes mitochondrial proteomes contains (i) endosymbiotic proteins (15-45%), (ii) proteins without detectable orthologs outside the eukaryotic lineage (40%), and (iii) proteins that are derived from non-proteobacterial Bacteria, Bacteriophages and Archaea (15%, specifically multiple tRNA-modification proteins). Protein complexes are of endosymbiotic origin, but have greatly expanded with novel eukaryotic proteins; in contrast to mitochondrial enzymes that are both of proteobacterial and non-proteobacterial origin. This disparity is consistent with the complexity hypothesis, which argues that proteins that are a part of large, multi-subunit complexes are unlikely to undergo horizontal gene transfer. We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do.     

Application of Physical Methods to the Study of Serum Lipoprotein

Abstract

One of the primary characteristics distinguishing prokaryotic from eukaryotic cells is the absence of a nucleus with a clearly defined nuclear membrane. In prokaryotic cells the DNA is condensed into a structure called the nucleoid. This structure has also been referred to attimes as the nuclear body, prokaryotic nucleus, bacterial chromosome, folded genome, or folded bacterial chromosome. The nomenclature sometimes becomes confusing because unfolded bacterial DNA free of other components of the nucleoid has also been referred to as the bacterial chromosome. To avoid such confusion, it would be preferable to reserve the terms nucleoid or bacterial chromosome to describe the condensed prokaryotic DNA structures which have some features analogous to the eukaryotic metaphase chromosome and condensed interphase chromatin. If this convention is followed, the terms “folded chromosome” or “folded genome” become ambiguous because they could equally mean “folded nucleoid.” These latter terms will, therefore, be avoided throughout this article.     

Evaluating hypotheses for the origin of eukaryotes

Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). We evaluate these hypotheses using the following three criteria. Can the data be explained by the null hypothesis that new features arise sequentially along a stem lineage? Second, hypotheses involving an archaeon and a bacterium should undergo standard phylogenetic tests of gene distribution. Third, accounting for past events by processes observed in modern cells is preferable to postulating unknown processes that have never been observed. For example, there are many eukaryote examples of bacteria as endosymbionts or endoparasites, but none known in archaea. Strictly post‐hoc hypotheses that ignore this third criterion should be avoided. Applying these three criteria significantly narrows the number of plausible hypotheses. Given current knowledge, our conclusion is that the eukaryote lineage must have diverged from an ancestor of archaea well prior to the origin of the mitochondrion. Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host. BioEssays 29: 74–84, 2007. © 2006 Wiley Periodicals, Inc.     

Demonstration of nucleomorph-encoded eukaryotic small subunit ribosomal RNA in cryptomonads

Summary In cryptomonads, unicellular phototrophic flagellates, the plastid(s) is (are) located in a special narrow compartment which is bordered by two membranes; it harbours neither mitochondria nor Golgi dictyosomes but comprises eukaryotic ribosomes and starch grains together with a small organelle called the nucleomorph. The nucleomorph contains DNA and is surrounded by a double membrane with pores. It is thought to be the vestigial nucleus of a phototrophic eukaryotic endosymbiont. Cryptomonads are therefore supposed to represent an intermediate state in the evolution of complex plastids from endosymbionts. We have succeeded in isolating pure nucleomorph fractions, and can thus provide, using pulsed field gel electrophoresis, polymerase chain reaction and sequence analysis, definitive proof for the eukaryotic nature of the symbiont and its phylogenetic origin.     

Rethinking plastid evolution

How easy is it to acquire an organelle? How easy is it to lose one? Michael Gray considers the latest evidence in this regard concerning the chromalveolates.How easy is it to acquire an organelle? How easy is it to lose one? These questions underpin the current debate about the evolution of the plastid—that is, chloroplast—the organelle of photosynthesis in eukaryotic cells.The origin of the plastid has been traced to an endosymbiosis between a eukaryotic host cell and a cyanobacterial symbiont, the latter gradually ceding genetic control to the former through endosymbiotic gene transfer (EGT). The resulting organelle now relies for its biogenesis and function on the expression of a small set of genes retained in the shrunken plastid genome, as well as a much larger set of transferred nuclear genes encoding proteins synthesized in the cytosol and imported into the organelle.This scenario accounts for the so-called primary plastids in green algae and their land plant relatives, in red algae and in glaucophytes, which together comprise Plantae (or Archaeplastida)—one of five or six recognized eukaryotic supergroups (Adl et al, 2005). In other algal types, plastids are ‘second-hand''—they have been acquired not by taking up a cyanobacterium, but by taking up a primary-plastid-containing eukaryote (sometimes a green alga, sometimes a red alga) to produce secondary plastids. In most of these cases, all that remains of the eukaryotic symbiont is its plastid; the genes coding for plastid proteins have moved from the endosymbiont to the host nucleus. A eukaryotic host—which may or may not itself have a plastid—might also take up a secondary-plastid symbiont (generating tertiary plastids), or a secondary-plastid host might take up a primary-plastid symbiont. You get the picture: plastid evolution is complicated!Several excellent recent reviews present expanded accounts of plastid evolution (Reyes-Prieto et al, 2007; Gould et al, 2008; Archibald, 2009; Keeling, 2009). Here, I focus on one particular aspect of plastid evolutionary theory, the ‘chromalveolate hypothesis'', proposed in 1999 by Tom Cavalier-Smith (1999).The chromalveolate hypothesis seeks to explain the origin of chlorophyll c-containing plastids in several eukaryotic groups, notably cryptophytes, alveolates (ciliates, dinoflagellates and apicomplexans), stramenopiles (heterokonts) and haptophytes—together dubbed the ‘chromalveolates''. The plastid-containing members of this assemblage are mainly eukaryotic algae with secondary plastids that were acquired through endosymbiosis with a red alga. The question is: how many times did such an endosymbiosis occur within the chromalveolate grouping?A basic tenet of the chromalveolate hypothesis is that the evolutionary conversion of an endosymbiont to an organelle should be an exceedingly rare event, and a hard task for a biological system to accomplish, because the organism has to ‘learn'' how to target a large number of nucleus-encoded proteins—the genes of many of which were acquired by EGT—back into the organelle. Our current understanding of this targeting process is detailed in the reviews cited earlier. Suffice it to say that the evolutionary requirements appear numerous and complex—sufficiently so that the chromalveolate hypothesis posits that secondary endosymbiosis involving a red alga happened only once, in a common ancestor of the various groups comprising the chromalveolates.Considerable molecular and phylogenetic data have been marshalled over the past decade in support of the chromalveolate hypothesis; however, no single data set specifically unites all chromalveolates, even though there is compelling evidence for various subgroup relationships (Keeling, 2009). Moreover, within the proposed chromalveolate assemblage, plastid-containing lineages are interspersed with plastid-lacking ones—for example, ciliates in the alveolates, and oomycetes such as Phytophthora in the stramenopiles. The chromalveolate hypothesis rationalizes such interspersion by assuming that the plastid was lost at some point during the evolution of the aplastidic lineages. The discovery in such aplastidic lineages of genes of putatively red algal origin, and in some cases suggestive evidence of a non-photosynthetic plastid remnant, would seem to be consistent with this thesis, although these instances are still few and far between.In this context, two recent papers are notable in that the authors seek to falsify, through rigorous testing, several explicit predictions of the chromalveolate hypothesis—and in both cases they succeed in doing so. Because molecular phylogenies have failed to either robustly support or robustly disprove the chromalveolate hypothesis, Baurain et al (2010) devised a phylogenomic falsification of the chromalveolate hypothesis that does not depend on full resolution of the eukaryotic tree. They argued that if the chlorophyll c-containing chromalveolate lineages all derive from a single red algal ancestor, then similar amounts of sequence from the three compartments should allow them to recover chromalveolate monophyly in all cases. The statistical support levels in their analysis refuted this prediction, leading them to “reject the chromalveolate hypothesis as falsified in favour of more complex evolutionary scenarios involving multiple higher order eukaryote–eukaryote endosymbioses”.In another study, Stiller et al (2009) applied statistical tests to several a priori assumptions relating to the finding of genes of supposed algal origin in the aplastidic chromalveolate taxon Phytophthora. These authors determined that the signal from these genes “is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution”.So, is the chromalveolate hypothesis dead? These new studies are certainly the most serious challenge yet. Additional data, including genome sequences of poorly characterized chromalveolate lineages, will no doubt augment comparative phylogenomic studies aimed at evaluating the chromalveolate hypothesis—which these days is looking decidedly shaky.     

Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes

Chaperonins are oligomeric protein-folding complexes which are divided into two distantly related structural classes. Group I chaperonins (called GroEL/cpn60/hsp60) are found in bacteria and eukaryotic organelles, while group II chaperonins are present in archaea and the cytoplasm of eukaryotes (called CCT/TriC). While archaea possess one to three chaperonin subunit-encoding genes, eight distinct CCT gene families (paralogs) have been characterized in eukaryotes. We are interested in determining when during eukaryotic evolution the multiple gene duplications producing the CCT subunits occurred. We describe the sequence and phylogenetic analysis of five CCT genes from TRICHOMONAS: vaginalis and seven from GIARDIA: lamblia, representatives of amitochondriate protist lineages thought to have diverged early from other eukaryotes. Our data show that the gene duplications producing the eight CCT paralogs took place prior to the organismal divergence of TRICHOMONAS: and GIARDIA: from other eukaryotes. Thus, these divergent protists likely possess completely hetero-oligomeric CCT complexes like those in yeast and mammalian cells. No close phylogenetic relationship between the archaeal chaperonins and specific CCT subunits was observed, suggesting that none of the CCT gene duplications predate the divergence of archaea and eukaryotes. The duplications producing the CCTdelta and CCTepsilon subunits, as well as CCTalpha, CCTbeta, and CCTeta, are the most recent in the CCT gene family. Our analyses show significant differences in the rates of evolution of archaeal chaperonins compared with the eukaryotic CCTs, as well as among the different CCT subunits themselves. We discuss these results in light of current views on the origin, evolution, and function of CCT complexes.     

Natural Signs and the Origin of Language

This article considers natural signs and their role in the origin of language. Natural signs, sometimes called primary signs, are connected with their signified by causal relationships, concomitance, or likeliness. And their acquisition is directed by both objective reality and past experience (memory). The discovery and use of natural signs is a required prerequisite of existence for any living systems because they are indispensable to movement, the search for food, regulation, communication, and many other information-related activities. It is argued that the birth of conventional signs, sometimes called secondary signs, was determined by a connotative use of natural signs and that, regulated and maintained by them, human language developed. At the same time, the origin and development of human language presupposes a ‘rational turn’ from the given and external reality of natural signs to the rationally constructed reality of artificial signs and rules that are internally maintained by the subjects’ deliberate activities, and actual and inherited social tradition (social memory). In view of this, language is defined as a dynamic system that must both be natural and artificial, empirical and a priori, inductive and deductive. This bilateral origin and regulation of language is the dual-inference of language.     

进化细胞生物学的提出及其任务

作者提出应创建一门源于进化生物学与细胞生物学两者的交叉学科一进化细胞生物学(细胞的进化生物学)。其根本任务在于用进化的观点考察真核细胞的一切方面,从它们的起源和演化来认识它们的现在。文中列举了其具体的研究内容,并分析了其研究方法上的特点,指出在这里需要把进化生物学的综合性分析与细胞生物学的实验研究最紧密地结合起来。文中还论述了真核细胞的细胞器的“不进化”现象,指出其根本原因在于进化焦点的转移。     

The origin of nucleus: rebuild from the prokaryotic ancestors of ribosome export factors

Various hypotheses have been proposed on the evolutionary origin of eukaryotic nucleus. Because one of the major cargoes in the nucleocytoplasmic export in the eukaryotic cell is the ribosome, its stimulating proteins called Ribosome Export Factors (REFs) might have an evolutionary history of inscribing the origin of eukaryotic nucleus. With the aim of understanding the evolutionary origin of the nucleus, here we employed the yeast REFs and searched for their evolutionary origin in more than 500 genomes of archaea and eubacteria by the PSI-BLAST search. Our results showed that the non-membranous REFs (non-mREFs) originated exclusively from eubacterial proteins, whereas the membranous REFs (mREFs) are from both archaeal and eubacterial proteins. Since the non-mREFs just work inside the nucleus while the mREFs shuttle between the nucleus and the cytoplasm, these results suggest that the extant REFs working inside the nucleus have derived exclusively from eubacterial proteins, implying that the nucleus arose in a cell that contained chromosomes possessing a substantial fraction of eubacterial genes, in line with the predictions of several models entailing endosymbiosis at eukaryote origins.     

The evolutionary origin of glycosomes

The glycolytic pathway of the Kinetoplastida is organized in a unique manner: the majority of its enzymes are contained in organelles called glycosomes. In this article Paul Michels and Fred Opperdoes argue that the glycosomes are equivalent to the microbodies and peroxisomes identified in other eukaryotic cells. They explore the possible evolutionary origin of the glycosome by comparing many of its structural and functional properties with those of other members of the microbody family and with some features of other organelles, the mitochondria and chloroplasts, which have been studied in much more detail.     

Evolution of ribosomal DNA-derived satellite repeat in tomato genome

Background  

Tandemly repeated DNA, also called as satellite DNA, is a common feature of eukaryotic genomes. Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated.     

The origin of eukaryotes: a reappraisal

Ever since the elucidation of the main structural and functional features of eukaryotic cells and subsequent discovery of the endosymbiotic origin of mitochondria and plastids, two opposing hypotheses have been proposed to account for the origin of eukaryotic cells. One hypothesis postulates that the main features of these cells, including their ability to capture food by endocytosis and to digest it intracellularly, were developed first, and later had a key role in the adoption of endosymbionts; the other proposes that the transformation was triggered by an interaction between two typical prokaryotic cells, one of which became the host and the other the endosymbiont. Re-examination of this question in the light of cell-biological and phylogenetic data leads to the conclusion that the first model is more likely to be the correct one.     

The number of symbiotic origins of organelles.

Mitochondria and chloroplasts both originated from bacterial endosymbionts. The available evidence strongly supports a single origin for mitochondria and only somewhat less strongly a single, slightly later, origin for chloroplasts. The arguments and evidence that have sometimes been presented in favor of the alternative theories of the multiple or polyphyletic origins of these two organelles are evaluated and the kinds of data that are needed to test more rigorously the monophyletic theory are discussed. Although chloroplasts probably originated only once, eukaryotic algae are polyphyletic because chloroplasts have been secondarily transferred to new lineages by the permanent incorporation of a photosynthetic eukaryotic algal cell into a phagotrophic protozoan host. How often this has happened is much less clear. It is particularly unclear whether or not the chloroplasts of typical dinoflagellates and euglenoids originated in this way from a eukaryotic symbiont: their direct divergence from the ancestral chloroplast cannot be ruled out and indeed has several arguments in its favor. The evidence for and against the view that the chloroplast of the kingdom Chromista was acquired in a single endosymbiotic event is discussed. The possibility that even the chloroplast of Chlorarachnion might have been acquired during the same symbiosis that created the cryptomonad cell, if the symbiont was a primitive alga that had chlorophyll a, b and c as well as phycobilins, is also considered. An alga with such a combination of pigments might have been ancestral to all eukaryote algae.