Isozyme analysis of theCerastium alpinum-C. arcticum complex (Caryophyllaceae) supports a splitting ofC. arcticum Lange

As part of a larger investigation of theC. alpinum-C. arcticum complex of arctic and North Atlantic areas, isozyme variation ofC. alpinum, C. arcticum, and related taxa was analysed. A total of 124 multilocus phenotypes was divided into more or less distinct groups by numerical analyses. Most groups correspond well to previously recognized taxa. However, what has traditionally been considered asC. arcticum was divided into two distinct groups, consisting of northern (Svalbard, Greenland) and more southern (Norway, Iceland) populations, respectively. The division ofC. arcticum into two taxa is also supported by other kinds of data and the two taxa probably deserve species rank. Serpentine plants from Shetland had multilocus phenotypes similar to those ofC. arcticum from Iceland and should be included in the southern taxon.     

Amoeboid properties of cells during early morphogenesis and the nature of a possible protozoan ancestor of Metazoa

Data analysis reveals that cells of most of the metazoans (especially from the phyla Spongia, Placozoa and Cnidaria) at the early stages of morphogenesis demonstrateas amoeboid properties i.e. ability to form pseudopodia, to move by means of pseudopodia and to phagocyte. In different degress these properties could be found at the late stages of embryogenesis and even in adult organisms. Moreover, during gastrulation and blastulation blastomeres is able to form flagellas and than loose them and return to amoeboid activity. These and other facts indicate that both amoeboid and flagellate types of cellular organization are programmed in the genome of metazoan cells, as well as their ability for mutual transformation. It leads to suggestion that ancestors of Metazoa were amoeboflagellates. Anarchic cleavage observed in some invertebrates evidences that separated blastomeres is able to aggregate into the unite embryo due to cytotaxis. Aggregation of artificially separated cells of sponges, trichoplax and cnidaria results in complete recovery of the organism by cytotaxis. Thus, there are reasons to suppose that ability of cell aggregation was inherited by the Metazoan genome from the amoeboflagellate ancestors. Thus amoeboflagellates may be considered as forerunners of Metazoa, i.e. Prometazoa.     

Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates

Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another eukaryote. But the number of times this has taken place is controversial. This is particularly so in the case of eukaryotes with plastids derived from red algae, which are numerous and diverse. Despite their diversity, it has been suggested that all these eukaryotes share a recent common ancestor and that their plastids originated in a single endosymbiosis, the so-called "chromalveolate hypothesis." Here we describe a novel molecular character that supports the chromalveolate hypothesis. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic and Calvin cycle enzyme that exists as two nonhomologous types, class I and class II. Red algal plastid-targeted FBA is a class I enzyme related to homologues from plants and green algae, and it would be predicted that the plastid-targeted FBA from algae with red algal secondary endosymbionts should be related to this class I enzyme. However, we show that plastid-targeted FBA of heterokonts, cryptomonads, haptophytes, and dinoflagellates (all photosynthetic chromalveolates) are class II plastid-targeted enzymes, completely unlike those of red algal plastids. The chromalveolate enzymes form a strongly supported group in FBA phylogeny, and their common possession of this unexpected plastid characteristic provides new evidence for their close relationship and a common origin for their plastids.     

Myxotrichum albicans,a new slowly-growing species isolated from forest litters in China

Myxotrichum albicans sp. nov. is a slowly-growing fungal species that was isolated from forest litters in northeast of China. The new species is morphologically characterized by its white colonies on CMA, PCA, PDA, and YMA, thallic conidiogenous cells, simple, catenate and hyaline conidia. Phylogenetic analysis based on internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences also supported the placement of M. albicans as a new species in the genus Myxotrichum. To compare with related species, the optimal pH and temperature for growth were investigated. The differences among Myxotrichum (Oidiodendron) species producing hyaline conidia were discussed.     

Chemotaxonomic consideration of flavonoids from the leaves of Chrysanthemum arcticum subsp. arcticum and yezoense,and related species

We examined the foliar flavonoids of Chrysanthemum arcticum subsp. arcticum and yezoense, and related Chrysanthemum species. Five flavonoid glycosides (luteolin 7-O-glucoside and 7-O-glucuronides of luteolin, apigenin, eriodictyol and naringenin) were isolated from these taxa. Luteolin 7-O-xylosylglucoside, luteolin, apigenin and quercetin 3-methyl ether were found in subsp. yezoense as very minor compounds that were not recognised by high-performance liquid chromatography/photodiode array (HPLC/PDA). The related species C. yezoense contained acacetin 7-O-rutinoside and some methoxylated flavone aglycones as major compounds. Thus, C. arcticum was distinguished from C. yezoense according to their flavonoid profiles.     

Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus

Many microsatellite loci contain more than a single repeat motif. These compound microsatellites are perhaps most easily explained as arising from simple ancestors. We have uncovered a contrary example in mice of the genus Mus. Sequence analysis of the locus D1MIT29 in most of the members of the genus Mus reveals that this locus is compound in all species except M. musculus, in which it is simple. Moreover, phylogenetic analyses of base substitutions in the non-repetitive flanking region gives trees which are consistent with the previously accepted phylogenetic hypothesis that M. musculus is nested within the subgenus Mus. This confirms that the history of this locus is similar to that of molecular markers previously used in phylogenetic studies of this group and, therefore, demonstrates that the simple state in this lineage is derived from a compound ancestor. We also demonstrate the utility of this type of nuclear sequence variation for phylogeographic studies in the genus Mus. Finally, our sequences reveal homoplasy for size, reemphasizing the danger of using microsatellite size variation alone when the individuals under study are not closely related. Received: 26 April 2000 / Accepted: 28 July 2000     

Experimental evolution of a facultative thermophile from a mesophilic ancestor

Experimental evolution via continuous culture is a powerful approach to the alteration of complex phenotypes, such as optimal/maximal growth temperatures. The benefit of this approach is that phenotypic selection is tied to growth rate, allowing the production of optimized strains. Herein, we demonstrate the use of a recently described long-term culture apparatus called the Evolugator for the generation of a thermophilic descendant from a mesophilic ancestor (Escherichia coli MG1655). In addition, we used whole-genome sequencing of sequentially isolated strains throughout the thermal adaptation process to characterize the evolutionary history of the resultant genotype, identifying 31 genetic alterations that may contribute to thermotolerance, although some of these mutations may be adaptive for off-target environmental parameters, such as rich medium. We undertook preliminary phenotypic analysis of mutations identified in the glpF and fabA genes. Deletion of glpF in a mesophilic wild-type background conferred significantly improved growth rates in the 43-to-48°C temperature range and altered optimal growth temperature from 37°C to 43°C. In addition, transforming our evolved thermotolerant strain (EVG1064) with a wild-type allele of glpF reduced fitness at high temperatures. On the other hand, the mutation in fabA predictably increased the degree of saturation in membrane lipids, which is a known adaptation to elevated temperature. However, transforming EVG1064 with a wild-type fabA allele had only modest effects on fitness at intermediate temperatures. The Evolugator is fully automated and demonstrates the potential to accelerate the selection for complex traits by experimental evolution and significantly decrease development time for new industrial strains.     

Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor

Summary The origin of plastids by either a single or multiple endosymbiotic event(s) and the nature of the progenitor(s) of plastids have been the subjects of much controversy. The sequence of the small subunit rRNA (Ssu rRNA) from the plastid of the chlorophyllc-containing algaCryptomonas is presented, allowing for the first time a comparison of this molecule from all of the major land plant and algal lineages. Using a distance matrix method, the phylogenetic relationships among representatives of these lineages have been inferred and the results indicate a common origin of plastids from a cyanobacterium-like ancestor. Within the plastid line of descent, there is a deep dichotomy between the chlorophyte/land plant lineage and the rhodophyte/chromophyte lineage, with the cyanelle ofCyanophora paradoxa forming the deepest branch in the latter group. Interestingly,Euglena gracilis and its colorless relativeAstasia longa are more related to the chromophytes than to the chlorophytes, raising once again the question of the origin of the euglenoid plastids.     

New species and records of saprophytic ascomycetes (Myxotrichaceae) from decaying logs in the boreal forest

Decayed wood from fallen white spruce (Picea glauca) and trembling aspen (Populus tremuloides) collected in northeastern Alberta, Canada, was the source of new isolates of species in the ascomycete generaGymnostellatospora andPseudogymnoascus. In addition to new reports ofG. japonica, G. frigida andP. roseus, two new species are described.Gymnostellatospora canadensis sp. nov. resemblesG. japonica but differs in producing brown ascomata and in the formation of an arthroconidial anamorph.Gymnostellatospora subnuda sp. nov. is distinct in lacking differentiated peridial hyphae.Gymnostellatospora alpina was not found in decayed wood but is reviewed based on extralimital material. A dichtomous key to the five species ofGymnostellatospora is provided.     

A preliminary study of the nutritional requirements of Myxotrichum uncinatum

Summary Certain nutritional requirements of one strain ofMyxotrichum uncinatum were established. Growth was measured on a dry weight basis. The approximate optimum medium for growth consisted of 5% KNO₃, 4% sucrose, 0.1% K₂HPO₄, 0.05% MgSO₄. 7 H₂O, 0.2 mg % biotin and 1.0 mg % uracil. The best initial pH range was 6.0–7.0. Approximately three to five days incubation on a rotary shaker permitted excellent growth.     

AGAMOUS‐LIKE13, a putative ancestor for the E functional genes,specifies male and female gametophyte morphogenesis

Arabidopsis AGL13 is a member of the AGL6 clade of the MADS box gene family. GUS activity was specifically detected from the initiation to maturation of both pollen and ovules in AGL13:GUS Arabidopsis. The sterility of the flower with defective pollen and ovules was found in AGL13 RNAi knockdown and AGL13 + SRDX dominant‐negative mutants. These results indicate that AGL13 acts as an activator in regulation of early initiation and further development of pollen and ovules. The production of similar floral organ defects in the severe AGL13 + SRDX and SEP2 + SRDX plants and the similar enhancement of AG nuclear localization efficiency by AGL13 and SEP3 proteins suggest a similar function for AGL13 and E functional SEP proteins. Additional fluorescence resonance energy transfer (FRET) analysis indicated that, similar to SEP proteins, AGL13 is able to interact with AG to form quartet‐like complexes (AGL13–AG)₂ and interact with AG–AP3–PI to form a higher‐order heterotetrameric complex (AGL13–AG–AP3–PI). Through these complexes, AGL13 and AG could regulate the expression of similar downstream genes involved in pollen morphogenesis, anther cell layer formation and the ovule development. AGL13 also regulates AG/AP3/PI expression by positive regulatory feedback loops and suppresses its own expression through negative regulatory feedback loops by activating AGL6, which acts as a repressor of AGL13. Our data suggest that AGL13 is likely a putative ancestor for the E functional genes which specifies male and female gametophyte morphogenesis in plants during evolution.     

Evolution of multinucleated Ashbya gossypii hyphae from a budding yeast-like ancestor

In the filamentous ascomycete Ashbya gossypii polarity establishment at sites of germ tube and lateral branch emergence depends on homologues of Saccharomyces cerevisiae factors controlling bud site selection and bud emergence. Maintenance of polar growth involves homologues of well-known polarity factors of budding yeast. To achieve the much higher rates of sustained polar surface expansion of hyphae compared to mainly non-polarly growing yeast buds five important alterations had to evolve. Permanent presence of the polarity machinery at a confined area in the rapidly expanding hyphal tip, increased cytoplasmic space with a much enlarged ER surface for generating secretory vesicles, efficient directed transport of secretory vesicles to and accumulation at the tip, increased capacity of the exocytosis system to process these vesicles, and an efficient endocytosis system for membrane and polarity factor recycling adjacent to the zone of exocytosis. Morphological, cell biological, and molecular aspects of this evolution are discussed based on experiments performed within the past 10 y.     

Genesis of Drosophila ADH: the shaping of the enzymatic activity from a SDR ancestor

Drosophila alcohol dehydrogenase (ADH) is an NAD(H)-dependent oxidoreductase that catalyzes the oxidation of alcohols and aldehydes. Structurally and biochemically distinct from all the reported ADHs (typically, the mammalian medium-chain dehydrogenase/reductase-ethanol-metabolizing enzyme), it stands as the only small-alcohol transforming system that has originated from a short-chain dehydrogenase/reductase (SDR) ancestor. The crystal structures of the apo, binary (E.NAD(+)) and three ternary (E.NAD(+).acetone, E.NAD(+).3-pentanone and E.NAD(+).cyclohexanone) forms of Drosophila lebanonensis ADH have allowed us to infer the structural and kinetic features accounting for the generation of the ADH activity within the SDR lineage.     

Evidence for a microRNA expansion in the bilaterian ancestor

Understanding how animal complexity has arisen and identifying the key genetic components of this process is a central goal of evolutionary developmental biology. The discovery of microRNAs (miRNAs) as key regulators of development has identified a new set of candidates for this role. microRNAs are small noncoding RNAs that regulate tissue-specific or temporal gene expression through base pairing with target mRNAs. The full extent of the evolutionary distribution of miRNAs is being revealed as more genomes are scrutinized. To explore the evolutionary origins of metazoan miRNAs, we searched the genomes of diverse animals occupying key phylogenetic positions for homologs of experimentally verified human, fly, and worm miRNAs. We identify 30 miRNAs conserved across bilaterians, almost double the previous estimate. We hypothesize that this larger than previously realized core set of miRNAs was already present in the ancestor of all Bilateria and likely had key roles in allowing the evolution of diverse specialist cell types, tissues, and complex morphology. In agreement with this hypothesis, we found only three, conserved miRNA families in the genome of the sea anemone Nematostella vectensis and no convincing family members in the genome of the demosponge Reniera sp. The dramatic expansion of the miRNA repertoire in bilaterians relative to sponges and cnidarians suggests that increased miRNA-mediated gene regulation accompanied the emergence of triploblastic organ-containing body plans. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor

While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins.     

The Ferritin-like superfamily: Evolution of the biological iron storeman from a rubrerythrin-like ancestor

Background

The Ferritins are part of the extensive ‘Ferritin-like superfamily’ which have diverse functions but are linked by the presence of a common four-helical bundle domain. The role performed by Ferritins as the cellular repository of excess iron is unique. In many ways Ferritins act as tiny organelles in their ability to secrete iron away from the delicate machinery of the cell, and then to release it again in a controlled fashion avoiding toxicity. The Ferritins are ancient proteins, being common in all three domains of life. This ubiquity reflects the key contribution that Ferritins provide in achieving iron homeostasis.

Scope of the review

This review compares the features of the different Ferritins and considers how they, and other members of the Ferritin-like superfamily, have evolved. It also considers relevant features of the eleven other known families within the Ferritin-like superfamily, particularly the highly diverse rubrerythrins.

Major conclusions

The Ferritins have travelled a considerable evolutionary journey, being derived from far more simplistic rubrerythrin-like molecules which play roles in defence against toxic oxygen species. The forces of evolution have moulded such molecules into three distinct types of iron storing (or detoxifying) protein: the classical and universal 24-meric ferritins; the haem-containing 24-meric bacterioferritins of prokaryotes; and the prokaryotic 12-meric Dps proteins. These three Ferritin types are similar, but also possess unique properties that distinguish them and enable then to achieve their specific physiological purposes.

General significance

A wide range of biological functions have evolved from a relatively simple structural unit.     

Genesis of Drosophila ADH: the shaping of the enzymatic activity from a SDR ancestor

Drosophila alcohol dehydrogenase (ADH) is an NAD(H)-dependent oxidoreductase that catalyzes the oxidation of alcohols and aldehydes. Structurally and biochemically distinct from all the reported ADHs (typically, the mammalian medium-chain dehydrogenase/reductase–ethanol-metabolizing enzyme), it stands as the only small-alcohol transforming system that has originated from a short-chain dehydrogenase/reductase (SDR) ancestor. The crystal structures of the apo, binary (E·NAD⁺) and three ternary (E·NAD⁺·acetone, E·NAD⁺·3-pentanone and E·NAD⁺·cyclohexanone) forms of Drosophila lebanonensis ADH have allowed us to infer the structural and kinetic features accounting for the generation of the ADH activity within the SDR lineage.     

Ontogenetic differences in heterostylous plants and implications for development from a herkogamous ancestor

Abstract.— Alternative ontogenetic pathways among heterostylous species of Rubiaceae may reflect differences in their evolutionary histories. In this study, measurements were taken at different developmental stages on a series of long-styled (LS) and short-styled (SS) buds of the heterostylous taxa Psychotria chiapensis, P. poeppigiana , and Bouvardia ternifolia (all Rubiaceae). Results indicated that modifications in growth rates of stamens relative to corollas in all three species led to differences in anther heights between LS and SS flowers. Distinct style heights for LS and SS flowers of P. chiapensis and P. poeppigiana originate in the earlier stages of bud development and are maintained as styles elongate at equal rates. This contrasts with B. ternifolia , which has differences in style heights resulting from unequal relative growth rates between floral morphs. The "approach herkogamous" floral morphology, defined by having stigmas positioned above anthers, has been proposed as a potential evolutionary precursor for heterostylous taxa. To examine this hypothesis, floral development of two species with approach herkogamous morphologies, Psychotria pittieri and P. brachiata , was compared to that of the three heterostylous taxa. Differences in the relative rates of style elongation for flowers of approach herkogamous versus heterostylous species predict additional steps in the original model for the evolution of heterostyly from an approach herkogamous ancestor. The diversity of heterostylous ontogenies found within Rubiaceae provides insight into potential evolutionary pathways for this sexual system in other angiosperm families.     

Evidence of a chimeric genome in the cyanobacterial ancestor of plastids

Background

Horizontal gene transfer (HGT) is a vexing fact of life for microbial phylogeneticists. Given the substantial rates of HGT observed in modern-day bacterial chromosomes, it is envisaged that ancient prokaryotic genomes must have been similarly chimeric. But where can one find an ancient prokaryotic genome that has maintained its ancestral condition to address this issue? An excellent candidate is the cyanobacterial endosymbiont that was harnessed over a billion years ago by a heterotrophic protist, giving rise to the plastid. Genetic remnants of the endosymbiont are still preserved in plastids as a highly reduced chromosome encoding 54 – 264 genes. These data provide an ideal target to assess genome chimericism in an ancient cyanobacterial lineage.

Results

Here we demonstrate that the origin of the plastid-encoded gene cluster for menaquinone/phylloquinone biosynthesis in the extremophilic red algae Cyanidiales contradicts a cyanobacterial genealogy. These genes are relics of an ancestral cluster related to homologs in Chlorobi/Gammaproteobacteria that we hypothesize was established by HGT in the progenitor of plastids, thus providing a 'footprint' of genome chimericism in ancient cyanobacteria. In addition to menB, four components of the original gene cluster (menF, menD, menC, and menH) are now encoded in the nuclear genome of the majority of non-Cyanidiales algae and plants as the unique tetra-gene fusion named PHYLLO. These genes are monophyletic in Plantae and chromalveolates, indicating that loci introduced by HGT into the ancestral cyanobacterium were moved over time into the host nucleus.

Conclusion

Our study provides unambiguous evidence for the existence of genome chimericism in ancient cyanobacteria. In addition we show genes that originated via HGT in the cyanobacterial ancestor of the plastid made their way to the host nucleus via endosymbiotic gene transfer (EGT).