Molecular evolutionary analysis based on the amino acid sequence of catalase

Heme-containing catalase sequences from 20 different organisms representing prokaryotes, fungi, animals, and plants have been compiled for phylogenetic reconstruction. Phylogenies based on distance and parsimony analysis show that fungal and animal catalases can be derived from one ancestor, whereas bacterial catalases fail to form a monophyletic group. Plant catalases appear to form a second class of catalases that arose independently from a possible prokaryotic ancestor.Correspondence to: P.C. Loewen     

Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members

Mammalian DNA polymerase (pol) β is the founding member of a large group of DNA polymerases now termed the X-family. DNA polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. Accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the X-family of DNA polymerases. The bacterial X-family DNA polymerases, Saccharomyces cerevisiae pol IV, and four mammalian X-family polymerases appear to be directly related. These enzymes originated from an ancient common ancestor characterized in two Bacillus species. Understanding distinct functions for each of the X-family polymerases, evolving from a common bacterial ancestor is of significant interest in light of the specialized roles of these enzymes in DNA metabolism.     

On Cretaceous bioconstructions: Composition and evolutionary trends of crust-building associations

Summary Bioconstructions are built by colonial to solitary sessile organisms which develop a variety of different morphologies due to genetic, ecologic, and environmental controls. Crust-building associations are groups of encrusting taxa within a community which predominantly serve as binders and cementers of bioconstructions (planooccupants), while constructing organisms predominantly build the frameworks (spatio-occupants). In the Cretaceous, the most important constructional elements were corals, stromatoporoids, chaetetids, and rudists which built thickets, biostromes, mounds, patch reefs, and occasionally bioherms. The crust-building associations were composed of corals, cyanophytes (including tubiphytoids), microproblematicum (Lithocodium/Bacinella), modern red algae (corallinaceans and peyssonneliceans), as well as some stromatoporoids and chaetetids. The combination of constructing and binding associations can be used to differentiate Cretaceous build-ups both temporally and in terms of ecologic succession. The development of tropical to subtropical carbonate platforms during the Cretaceous brought about a world-wide expansion of and innovation within bioconstructions. The major changes within bioconstructions consist of the increasing dominance of the rudists as framework constructors and the evolution of the modern red algae. The corals remained an essential element of reef constructional as well as of binding associations. The stromatoporoids and chaetetids, however, lost importance during the mid-Cretaceous. Other important qualitative changes were the evolution of the acervulinids (a massive encrusting foraminiferid) during Campanian to Maastrichtian time and the extinction of the rudists at the end of the Cretaceous. Cretaceous bioconstructions suffered significant periods of retrogradation during the following periods: the beginning of the Cretaceous, Cenomanian-Turonian, and Maastrichtian-Paleocene. These represent long-term evolutionary changes, and to date, there is at least for encrusting associations no evidence to corroborate the short-term mass extinction events commonly documented for these boundaries. These long-term changes appear to be controlled by the interaction of various over-riding factors (tectonism, paleogeographic changes, oceanic chemistry, climate, and sea-level fluctuations). Although for individual bioconstructions the primary controlling mechanisim can possibly be determined, this is impossible at a global scale given current levels of understanding of the intricate interactions of these various factors.     

Use of structural phylogenetic networks for classification of the ferritin-like superfamily

In the postgenomic era, bioinformatic analysis of sequence similarity is an immensely powerful tool to gain insight into evolution and protein function. Over long evolutionary distances, however, sequence-based methods fail as the similarities become too low for phylogenetic analysis. Macromolecular structure generally appears better conserved than sequence, but clear models for how structure evolves over time are lacking. The exponential growth of three-dimensional structural information may allow novel structure-based methods to drastically extend the evolutionary time scales amenable to phylogenetics and functional classification of proteins. To this end, we analyzed 80 structures from the functionally diverse ferritin-like superfamily. Using evolutionary networks, we demonstrate that structural comparisons can delineate and discover groups of proteins beyond the "twilight zone" where sequence similarity does not allow evolutionary analysis, suggesting that considerable and useful evolutionary signal is preserved in three-dimensional structures.     

Multiple evolutionary origins lead to diversity in the metabolic profiles of ambrosia fungi

Ambrosia fungi are an ecological assemblage cultivated by ambrosia beetles as required nutrient sources. This mutualism evolved in multiple beetle and fungus lineages. Whether convergence in ecology led to convergent metabolism in ambrosia fungi is unknown. We compared the assimilation of 190 carbon sources in five independent pairs of ambrosia fungi and closely related, non-ambrosial species. Ecological convergence versus phylogenetic divergence in carbon source use was tested using variation partitioning. We found no convergence in carbon utilization capacities. Instead, metabolic variation was mostly explained by phylogenetic relationships. In addition, carbon usage in ambrosia fungi was equally diverse as that in non-ambrosial species. Thus, carbon metabolism of each ambrosia fungus is determined by its inherited metabolism, not the transition towards symbiosis. In contrast to other fungus-farming systems of termites and attine ants, the fungal symbionts of ambrosia beetles are functionally diverse, reflecting their independent evolutionary origins.     

Spermatozoa of murid rodents from Africa: morphological diversity and evolutionary trends

The diversity of the structural organization of the spermatozoa of African murid rodents is described at the light and transmission electron microscopical level of resolution. In most species the sperm head is falciform in shape but it varies somewhat in overall breadth, width, and length. A typical perforatorium is present and the acrosome splits into a large head cap over the convex surface and a smaller ventral segment similar to the sperm head of most Asian and Australasian murids. In a few species, however, the morphology is very different. In Acomys and Uranomys spermatozoa, the apical hook is more bilaterally flattened, has a large apical acrosomal region, and no separate ventral segment. Two species of Aethomys have, in addition to an apical hook, a 4μ long extension of the cytoskeletal material that projects from the concave surface of the sperm head, whereas in Dasymys two large ventral processes extend from the upper concave region which contain nuclear material basally and a huge extension of cytoskeleton apically. In Aethomys chrysophilus type B, the sperm nucleus is unique in form and often has a central region in which threads of chromatin can be seen; it is capped by a massive acrosome whose apical segment is complex and convoluted in structure. Stochomys longicaudatus appears to have a conical sperm head, and in all three Lophuromys species the sperm head is spatulate in shape with the flat, plate-like nucleus capped by a thin acrosome. The evolutionary trends in changes of sperm head shape and design of these rodents are discussed. It is suggested that some of the differences in morphology may relate to the variation in structural organization of the coats around the egg through which the spermatozoon has to pass in order for fertilization to occur.     

Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes: A Theoretical Study

Abstract

We use a recently developed formalism (1) to calculate the salt dependent part of the free energy determining DNA conformational stability in 1:1 electrolytes. The conformations studied are the A,B,C and alternating-B right-handed forms and the Z₁Z_II left-handed forms of DNA. In the case of the B-Z₁ transition of d(G-C) · d(G-C) helices in NaCl solution, the free energy contribution considered suffices to describe the transition in a quantitative manner. The theory also predicts the occurrence of salt-induced B-A transitions which have been recently observed with poly[d(n²A-T)| and poly[d(G-C)|. In other cases, additional terms in the free energy balance, particularly due to hydration effects, must be at least as important as salt effects in determining conformational stability and structural transitions in solution. If diffuse ionic cloud electrostatic effects alone would dominate in all cases, the relative helical stabilities at 0.2 M monovalent salt would decrease in the order C > B > A > Z_II > Z₁ > alternating-B. At high salt concentrations (2.0 M - 5.0 M), the order would be alternating-B > Z, > A > Z_II > B > C.     

Diversity of brood chambers in calloporid bryozoans (Gymnolaemata,Cheilostomata): comparative anatomy and evolutionary trends

Comparative anatomical studies of 12 species from 10 genera (Callopora, Tegella, Amphiblestrum, Parellisina, Corbulella, Crassimarginatella, Valdemunitella, Bryocalyx, Concertina, Cauloramphus) belonging to one of the largest and most diverse bryozoan taxa, the Calloporidae, and one species from the genus Akatopora belonging to the related taxon Antroporidae, were undertaken to elucidate the morphological diversity of brooding structures and to recognize main trends in their evolution. Most of the species studied possess ovicells (specialized brooding receptacles) formed by the distal and maternal (egg-producing) autozooids. The distal zooid can be an autozooid, a vicarious avicularium or a kenozooid. The calcified protective hood (ooecium) is an outgrowth from the distal zooid. Hyperstomial or prominent ovicells are most common. They were found in species of the genera Callopora, Tegella, Amphiblestrum, Parellisina, Corbulella, Bryocalyx and Concertina. Subimmersed ovicells were found in Valdemunitella, and immersed ovicells in Crassimarginatella and Akatopora. Cauloramphus has an internal brooding sac and a vestigial kenozooidal ooecium, budded by the maternal zooid. Based on the structure of the brooding organs, the following evolutionary trends can be recognized within the group: (1) reduction of the distal (ooecium-producing) zooid, (2) immersion of the brooding cavity correlated with a reduction of the ooecium and ooecial vesicle and with changes in the ovicell closure and the structure of the brood chamber floor, (3) reduction of the calcification of the ectooecium, and (4) transition from bilobate to entire ooecium. The trend towards immersion of the brooding cavity could have evolved repeatedly within the Calloporidae. Transition from bilobate to entire ooecium is characteristic of the related taxon Cribrilinidae, showing a good example of parallel evolution of the ooecium in two closely related clades. Possible causes for the transformations described are discussed.     

The role of peroxisomes in the integration of metabolism and evolutionary diversity of photosynthetic organisms

The peroxisome is a metabolic compartment serving for the rapid oxidation of substrates, a process that is not coupled to energy conservation. In plants and algae, peroxisomes connect biosynthetic and oxidative metabolic routes and compartmentalize potentially lethal steps of metabolism such as the formation of reactive oxygen species and glyoxylate, thus preventing poisoning of the cell and futile recycling. Peroxisomes exhibit properties resembling inside-out vesicles and possess special systems for the import of specific proteins, which form multi-enzyme complexes (metabolons) linking numerous reactions to flavin-dependent oxidation, coupled to the decomposition of hydrogen peroxide by catalase. Hydrogen peroxide and superoxide originating in peroxisomes are important mediators in signal transduction pathways, particularly those involving salicylic acid. By contributing to the synthesis of oxalate, formate and other organic acids, peroxisomes regulate major fluxes of primary and secondary metabolism. The evolutionary diversity of algae has led to the presence of a wide range of enzymes in the peroxisomes that are only similar to higher plants in their direct predecessors, the Charophyceae. The appearance of seed plants was connected to the acquirement by storage tissues, of a peroxisomal fatty acid oxidation function linked to the glyoxylate cycle, which is induced during seed germination and maturation. Rearrangement of the peroxisomal photorespiratory function between different tissues of higher plants led to the appearance of different types of photosynthetic metabolism. The peroxisome may therefore have played a key role in the evolutionary formation of metabolic networks, via establishing interconnections between different metabolic compartments.     

Exploring the evolutionary diversity and assembly modes of multi-aminoacyl-tRNA synthetase complexes: Lessons from unicellular organisms

Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and ancient enzymes, mostly known for their essential role in generating aminoacylated tRNAs. During the last two decades, many aaRSs have been found to perform additional and equally crucial tasks outside translation. In metazoans, aaRSs have been shown to assemble, together with non-enzymatic assembly proteins called aaRSs-interacting multifunctional proteins (AIMPs), into so-called multi-synthetase complexes (MSCs). Metazoan MSCs are dynamic particles able to specifically release some of their constituents in response to a given stimulus. Upon their release from MSCs, aaRSs can reach other subcellular compartments, where they often participate to cellular processes that do not exploit their primary function of synthesizing aminoacyl-tRNAs. The dynamics of MSCs and the expansion of the aaRSs functional repertoire are features that are so far thought to be restricted to higher and multicellular eukaryotes. However, much can be learnt about how MSCs are assembled and function from apparently ‘simple’ organisms. Here we provide an overview on the diversity of these MSCs, their composition, mode of assembly and the functions that their constituents, namely aaRSs and AIMPs, exert in unicellular organisms.     

The evolutionary potential of paramutation: A population-epigenetic model

Paramutation involves an interaction between homologous alleles resulting in a heritable change in gene expression without altering the DNA sequence. Initially believed to be restricted to plants, paramutation has recently been observed in animal models, and a paramutation-like event has been noted in humans. Despite the accumulating evidence suggesting that trans-acting epigenetic effects can be inherited transgenerationally and therefore generate non-genomic phenotypic variation, these effects have been largely ignored in the context of evolutionary theory. The model presented here incorporates paramutation into the standard model of viability selection at one locus and demonstrates that paramutation can create long-term biological diversity in the absence of genetic change, and even in the absence of the original paramutagenic allele. Therefore, if paramutation is present, attributing evolution to only a traditional genetic model may fail to encompass the broad scope of phenotypic differences observed in nature. Moreover, we show also that an unusual mathematical behaviour, analogous to “Ewens’ gap” of the two-locus two-allele symmetric-selection model, occurs: when the rate of one parameter–for example, the rate of paramutation–is increased, a pair of equilibria may disappear only to reappear as this parameter increases further. In summary, by incorporating even the simplest epigenetic parameters into the standard population-genetic model of selection, we show how this type of inheritance system can profoundly alter the course of evolution.     

Compartmentalized isozyme genes and the origin of introns

Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10^–3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.     

Genotype distribution and evolutionary analysis of rotavirus associated with acute diarrhea outpatients in Hubei,China, 2013–2016

Group A human rotaviruses (RVAs) annually cause the deaths of 215,000 infants and young children. To understand the epidemiological characteristics and genetic evolution of RVAs, we performed sentinel surveillance on RVA prevalence in a rotavirus-surveillance network in Hubei, China. From 2013 to 2016, a total of 2007 fecal samples from hospital outpatients with acute gastroenteritis were collected from four cities of Hubei Province. Of the 2007 samples, 153 (7.62%) were identified positive for RVA by real-time RT-PCR. RVA infection in Hubei mainly occurred in autumn and winter. The highest detection rate of RVA infection was in 1–2 years old of outpatients (16.97%). No significant difference of RVA positive rate was observed between females and males. We performed a phylogenetic analysis of the G/P genotypes based on the partial VP7/VP4 gene sequences of RVAs. G9P[8] was the most predominant strain in all four years but the prevalence of G2P[4] genotype increased rapidly since 2014. We reconstructed the evolutionary time scale of RVAs in Hubei, and found that the evolutionary rates of the G9, G2, P[8], and P[4] genotypes of RVA were 1.069 ​× ​10⁻³, 1.029 ​× ​10⁻³, 1.283 ​× ​10⁻³ and 1.172 ​× ​10⁻³ nucleotide substitutions/site/year, respectively. Importantly, using a molecular clock model, we showed that most G9, G2, P[8], and P[4] genotype strains dated from the recent ancestor in 2005, 2005, 1993, and 2013, respectively. The finding of the distribution of RVAs in infants and young children in Hubei Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of RVAs in China.     

Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex

Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.     

Widespread occurrence of the Tc1 transposon family: Tc1-like transposons from teleost fish

We characterized five transposable elements from fish: one from zebrafish (Brachydanio rerio), one from rainbow trout (Salmo gairdneri), and three from Atlantic salmon (Salmo salar). All are closely similar in structure to the Tel transposon of the nematode Caenorhabditis elegans. A comparison of 17 Tc1-like transposons from species representing three phyla (nematodes, arthropods, and chordates) showed that these elements make up a highly conserved transposon family. Most are close to 1.7 kb in length, have inverted terminal repeats, have conserved terminal nucleotides, and each contains a single gene encoding similar poly peptides. The phylogenetic relationships of the transposons were reconstructed from the amino acid sequences of the conceptual proteins and from DNA sequences. The elements are highly diverged and have evidently inhabited the genomes of these diverse species for a long time. To account for the data, it is not necessary to invoke recent horizontal transmission.     

Hidden diversity and evolutionary trends in malacosporean parasites (Cnidaria: Myxozoa) identified using molecular phylogenetics

Malacosporeans represent a small fraction of myxozoan biodiversity with only two genera and three species described. They cycle between bryozoans and freshwater fish. In this study, we (i) microscopically examine and screen different freshwater/marine fish species from various geographic locations and habitats for the presence of malacosporeans using PCR; (ii) study the morphology, prevalence, host species/habitat preference and distribution of malacosporeans; (iii) perform small subunit/large subunit rDNA and Elongation factor 2 based phylogenetic analyses of newly gathered data, together with all available malacosporean data in GenBank; and (iv) investigate the evolutionary trends of malacosporeans by mapping the morphology of bryozoan-related stages, host species, habitat and geographic data on the small subunit rDNA-based phylogenetic tree. We reveal a high prevalence and diversity of malacosporeans in several fish hosts in European freshwater habitats by adding five new species of Buddenbrockia and Tetracapsuloides from cyprinid and perciform fishes. Comprehensive phylogenetic analyses revealed that, apart from Buddenbrockia and Tetracapsuloides clades, a novel malacosporean lineage (likely a new genus) exists. The fish host species spectrum was extended for Buddenbrockia plumatellae and Buddenbrockia sp. 2. Co-infections of up to three malacosporean species were found in individual fish. The significant increase in malacosporean species richness revealed in the present study points to a hidden biodiversity in this parasite group. This is most probably due to the cryptic nature of malacosporean sporogonic and presporogonic stages and mostly asymptomatic infections in the fish hosts. The potential existence of malacosporean life cycles in the marine environment as well as the evolution of worm- and sac-like morphology is discussed. This study improves the understanding of the biodiversity, prevalence, distribution, habitat and host preference of malacosporeans and unveils their evolutionary trends.     

Burrowing behavior of Dermatonotus muelleri (Anura,Microhylidae) with reference to the origin of the burrowing behavior of Anura

Dermatonotus muelleri is a forelimbs-head-first burrowing frog that uses its forelimbs for soil removal, and it is the second anuran species known to arch its head downwards at an angle of almost 90° to the longitudinal axis of its body when burrowing. The burrowing behavior of D. muelleri is divided in three stages: head burrowing, body burrowing, and chamber construction. Burrowing in D. muelleri includes construction of a subterranean chamber used for estivation during the dry season. Phylogenetic analysis based on literature survey of burrowing behavior suggested that head-first burrowing behavior has evolved several times in anuran history, forming a convergence complex, and that hindlimbs-first burrowing is a basal behavior.     

Occurrence and ecological characteristics of C4 dicot and Cyperaceae species in the Hungarian flora

The non-graminaceous wild flora of Hungary was screened for C₄ plants by using the stable carbon isotope ratio, the leaf anatomy and the photosynthetic carbon dioxide compensation concentration to determine the photosynthetic pathway type. On the whole, 31 C₄ species (native or naturalized) were found in the Amaranthaceae, Chenopodiaceae, Cyperaceae, Euphorbiaceae, Portulacaceae and Zygophyllaceae families. Together with the 26 C₄ grass species (Poaceae) reported earlier (Kalapos 1991), a total of 57 wild C₄ species occur in Hungary, which forms 2.6 % of the country's angiosperm flora. This figure is somewhat higher than what was expected on climatic grounds, a fact probably due to certain edaphic conditions favouring C₄ plant growth. In Hungary, the C₄ species are predominantly annuals growing in open habitats such as dry grasslands, inland saline areas, temporarily exposed riverbeds and disturbed sites. In comparison with C₃ plants, the C₄ species have higher temperature and light preferences, and their phenology lags behind that of the C₃ plants. These differences might account for C₄ plants being usually excluded from productive biotopes in Hungary, where the C₃ canopy may become closed during the growing season before C₄ plants can start their ontogenetic development. Ecological properties of C₃ and C₄ plants differ considerably in the Cyperaceae, but much less in the Chenopodianceae family. Among C₄ annuals naturalized aliens are common, most of which colonized hungary in the last two centuries. Increasing preponderance of C₄ plants is anticipated in the future as a consequence of possible climate changes and the ever increasing human impact on terrestrial vegetation. This revised version was published online in August 2006 with corrections to the Cover Date.     

The diversity of nuclear cycle in microcyclic rust fungi (Uredinales) and its ecological and evolutionary implications

 Nine types with 11 variations of nuclear cycle and associated metabasidium development were distinguished in microcyclic rust fungi. An additional type was recognized in rust fungi with an expanded life cycle. A significant proportion of rust fungi with a reduced life cycle is assumed to have lost a sexual genetic recombination process, being either apomictic or asexual in reproduction. Most species that retain a sexual process in the microcyclic life cycle seem to have become homothallic. During life cycle evolution by the omission of spore stages, these traits might have had a selective advantage for those species that had less opportunity to encounter a genetically different but sexually compatible mate because of isolated patchy distribution or a short growing season. The findings that different populations of a morphologically identifiable species exhibit two or more distinct patterns of nuclear cycle and different metabasidium development indicate that microcyclic lineages might have evolved independently and repeatedly from a macrocyclic parental species. Those lineages are morphologically the same but would differ from each other in their genetics and biology. Received: July 5, 2002 / Accepted: August 5, 2002 Acknowledgment This work was supported in part by a Grant-in-Aid for Scientific Research (no. 09640744) from the Ministry of Education, Science and Culture (now the Ministry of Education, Culture, Sports, Science and Technology), Japan. Correspondence to:Y. Ono