Current trends in the structure-activity relationships of sialyltransferases

Sialyltransferases (STs) represent an important group of enzymes that transfer N-acetylneuraminic acid (Neu5Ac) from cytidine monophosphate-Neu5Ac to various acceptor substrates. In higher animals, sialylated oligosaccharide structures play crucial roles in many biological processes but also in diseases, notably in microbial infection and cancer. Cell surface sialic acids have also been found in a few microorganisms, mainly pathogenic bacteria, and their presence is often associated with virulence. STs are distributed into five different families in the CAZy database (http://www.cazy.org/). On the basis of crystallographic data available for three ST families and fold recognition analysis for the two other families, STs can be grouped into two structural superfamilies that represent variations of the canonical glycosyltransferase (GT-A and GT-B) folds. These two superfamilies differ in the nature of their active site residues, notably the catalytic base (a histidine or an aspartate residue). The observed structural and functional differences strongly suggest that these two structural superfamilies have evolved independently.     

An alternative classification of trypanorhynch cestodes considering the tentacular armature as being of limited importance

Based on a light- and scanning electron microscopical study of scolex morphology, tentacles and surface structures of 31 trypanorhynch species, an alternative classification of the trypanorhynch cestodes, adults, plerocerci and postlarvae, is presented. The arrangement of the tentacular armature is no longer used as a distinguishing feature for four different superfamilies. Instead, the presence or absence of ciliated pits and prebulbular organs is used to define three superfamilies: Tentacularioidea Poche, 1926; Otobothrioidea Dollfus, 1942; and Eutetrarhynchoidea Guiart, 1927. A total of 12 families are defined by the characters: the presence/absence of blastocysts, the number of bothridia and the reduction of the rhyncheal apparatus, together with a new character, complete rows of tentacular hooks (homeoacanth and heteroacanth typica) versus rows of hooks partly reduced (heteroacanth atypica and poeciloacanth). Of the 19 families previously accepted, 10 are retained (Eutetrarhynchidae, Gilquiniidae, Lacistorhynchidae, Mixodigmatidae, Otobothriidae, Paranybeliniidae, Pterobothriidae, Shirleyrhynchidae, Sphyriocephalidae and Tentaculariidae, all sensu nov.); one family is reinstated (i.e. Aporhynchidae Poche, 1926 sensu nov.) and a new one is added (i.e. Pseudotobothriidae n. fam.). Advantages of this alternative classification of trypanorhynch cestodes are: (i) the resolution of incongruities and questions caused by the use of the tentacular armature to distinguish superfamilies; (ii) the criteria for the establishment of higher taxa, superfamilies and families are clearly defined; (iii) with the findings of new species with different character combinations, this system can be enlarged up to 4 superfamilies and 48 families without loosing its stability; and (iv) all existing genera are easily re-assigned to the superfamilies and families.     

Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies

Glycosyltransferases (GTs) are diverse enzymes organized into 65 families. X-ray crystallography and in silico studies have shown many of these to belong to two structural superfamilies: GT-A and GT-B. Through application of fold recognition and iterated sequence searches, we demonstrate that families 60, 62, and 64 may also be grouped into the GT-A fold superfamily. Analysis of conserved acidic residues suggests that catalytic sites are better conserved in superfamily GT-B than in GT-A. Although 26% and 29% of GT families may now be confidently placed in superfamilies GT-A and GT-B, respectively, the remaining 45% of families bear no discernible resemblance to either superfamily, which, given the sensitivity of modern fold recognition methods, suggests the existence of novel structural scaffolds associated with GT activity. Furthermore, bioinformatics studies indicate the apparent ease with which mechanism-inverting or retaining-may change during evolution.     

SUPFAM: A database of sequence superfamilies of protein domains

Background  

SUPFAM database is a compilation of superfamily relationships between protein domain families of either known or unknown 3-D structure. In SUPFAM, sequence families from Pfam and structural families from SCOP are associated, using profile matching, to result in sequence superfamilies of known structure. Subsequently all-against-all family profile matches are made to deduce a list of new potential superfamilies of yet unknown structure.     

A galaxy of folds

Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co‐occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains.     

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs

MotifCluster finds related motifs in a set of sequences, and clusters the sequences into families using the motifs they contain. MotifCluster, at , lets users test whether proteins are related, cluster sequences by shared conserved motifs, and visualize motifs mapped onto trees, sequences and three-dimensional structures. We demonstrate MotifCluster's accuracy using gold-standard protein superfamilies; using recommended settings, families were assigned to the correct superfamilies with 0.17% false positive and no false negative assignments.     

Molecular phylogeny of the Calanoida (Crustacea: Copepoda)

The order Calanoida includes some of the most successful planktonic groups in both marine and freshwater environments. Due to the morphological complexity of the taxonomic characters in this group, subdivision and phylogenies have been complex and problematic. This study establishes a multi-gene molecular phylogeny of the calanoid copepods based upon small (18S) and large (28S) subunits of nuclear ribosomal RNA genes and mitochondrial encoded cytochrome b and cytochrome c oxidase subunit-I genes, including 29 families from 7 superfamilies of the order. This analysis is more comprehensive than earlier studies in terms of number of families, range of molecular markers, and breadth of taxonomic levels resolved. Patterns of divergence of ribosomal RNA genes are shown to be significantly heterogeneous among superfamilies, providing a likely explanation for disparate results of previous studies. The multi-gene phylogeny recovers a monophyletic Calanoida, as well as the superfamilies Augaptiloidea, Centropagoidea, Bathypontioidea, Eucalanoidea, Spinocalanoidea and Clausocalanoidea. The phylogeny largely agrees with previously-published morphological phylogenies, including e.g., enlargement of the Bathypontioidea to include the Fosshageniidae.     

Pathways of transport protein evolution: recent advances

We herein report recent advances in our understanding of transport protein evolution. Numerous families of complex transmembrane transport proteins are believed to have arisen from short channel-forming amphipathic or hydrophobic peptides by various types of intragenic duplication events. Distinct pathways distinguish families, demonstrating independent origins for some, and allowing assignment of others to superfamilies. Some families have diversified in topology, whereas others have remained uniform. An example of 'retroevolution' was discovered where a more complex carrier gave rise to a structurally and functionally simpler channel. The results described in this review article expand our understanding of protein evolution.     

Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds

Background

As tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. We consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. Do these domains represent an unbiased random sample of all sequence families? Do targets solved by structural genomic initiatives (SGI) provide such a sample? What are approximate total numbers of structure-based superfamilies and folds among soluble globular domains?

Results

To make these assessments, we combine two approaches: (i) sequence analysis and homology-based structure prediction for proteins from complete genomes; and (ii) monitoring dynamics of the assigned structure set in time, with the accumulation of experimentally solved structures. In the Clusters of Orthologous Groups (COG) database, we map the growing population of structurally characterized domain families onto the network of sequence-based connections between domains. This mapping reveals a systematic bias suggesting that target families for structure determination tend to be located in highly populated areas of sequence space. In contrast, the subset of domains whose structure is initially inferred by SGI is similar to a random sample from the whole population. To accommodate for the observed bias, we propose a new non-parametric approach to the estimation of the total numbers of structural superfamilies and folds, which does not rely on a specific model of the sampling process. Based on dynamics of robust distribution-based parameters in the growing set of structure predictions, we estimate the total numbers of superfamilies and folds among soluble globular proteins in the COG database.

Conclusion

The set of currently solved protein structures allows for structure prediction in approximately a third of sequence-based domain families. The choice of targets for structure determination is biased towards domains with many sequence-based homologs. The growing SGI output in the future should further contribute to the reduction of this bias. The total number of structural superfamilies and folds in the COG database are estimated as ~4000 and ~1700. These numbers are respectively four and three times higher than the numbers of superfamilies and folds that can currently be assigned to COG proteins.     

Taxonomic and structural similarities in soil oribatid communities

We examined the taxonomic and structural concordance between oribatid mite communities at different sites from around the world using meta-analysis. The study explored similarities in the taxonomie composition and species abundance distributions among oribatid mite communities using 25 published species lists from Africa, Australia, Europe. Japan. Malaysia, New Zealand and the United States, The final data set contained 253 genera from 97 families in 43 superfamilies, A second data set, which included only studies where trees were present at the sites, contained 234 genera, 93 families and 41 superfamilies. Composition was analysed at taxonomic levels higher than species. Only two families and four superfamilies were present in > 90% of all studies. Two genera, six families and seven superfamilies were found in all sites with trees. Common families were different among habitats suggesting that habitat preferences may be expressed at the family level. There were very strong relationships between oribatid mite species richness and richness at higher taxonomic levels with r² values for regression relationships > 0.8. Few species at a site were from the same genus, family or superfamily. Species abundance distributions were remarkably consistent between studies with the three most dominant species each constituting > 10% of the oribatid individuals. Overall, similar factors may determine the relative proportions of soil-dwelling oribatid species at a site.     

Divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases

We discuss the basic features of divergent versus convergent evolution and of the common scenario of parallel evolution. The example of quorum-quenching lactonases is subsequently described. Three different quorum-quenching lactonase families are known, and they belong to three different superfamilies. Their key active-site architectures have converged and are strikingly similar. Curiously, a promiscuous organophosphate hydrolase activity is observed in all three families. We describe the structural and mechanistic features that underline this converged promiscuity and how this promiscuity drove the parallel divergence of organophosphate hydrolases within these lactonase families by either natural or laboratory evolution.     

Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway.

BACKGROUND: Are folding pathways conserved in protein families? To test this explicitly and ask to what extent structure specifies folding pathways requires comparison of proteins with a common fold. Our strategy is to choose members of a highly diverse protein family with no conservation of function and little or no sequence identity, but with structures that are essentially the same. The immunoglobulin-like fold is one of the most common structural families, and is subdivided into superfamilies with no detectable evolutionary or functional relationship. RESULTS: We compared the folding of a number of immunoglobulin-like proteins that have a common structural core and found a strong correlation between folding rate and stability. The results suggest that the folding pathways of these immunoglobulin-like proteins share common features. CONCLUSIONS: This study is the first to compare the folding of structurally related proteins that are members of different superfamilies. The most likely explanation for the results is that interactions that are important in defining the structure of immunoglobulin-like proteins are also used to guide folding.     

Superfamilies SDR and MDR: From early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities

Two large gene and protein superfamilies, SDR and MDR (short- and medium-chain dehydrogenases/reductases), were originally defined from analysis of alcohol and polyol dehydrogenases. The superfamilies contain minimally 82 and 25 genes, respectively, in humans, minimally 324 and 86 enzyme families when known lines in other organisms are also included, and over 47,000 and 15,000 variants in existing sequence data bank entries. SDR enzymes have one-domain subunits without metal and MDR two-domain subunits without or with zinc, and these three lines appear to have emerged in that order from the universal cellular ancestor. This is compatible with their molecular architectures, present multiplicity, and overall distribution in the kingdoms of life, with SDR also of viral occurrence. An MDR-zinc, when present, is often, but not always, catalytic. It appears also to have a structural role in inter-domain interactions, coenzyme binding and substrate pocket formation, as supported by domain variability ratios and ligand positions. Differences among structural and catalytic zinc ions may be relative and involve several states. Combined, the comparisons trace evolutionary properties of huge superfamilies, with partially redundant enzymes in cellular redox functions.     

Evolution of protein superfamilies and bacterial genome size

We present the structural annotation of 56 different bacterial species based on the assignment of genes to 816 evolutionary superfamilies in the CATH domain structure database. These assignments have enabled us to analyse the recurrence of specific superfamilies within and across the genomes. We have selected the superfamilies that have a very broad representation and therefore appear to be universally distributed in a significant number of bacterial lineages. Occurrence profiles of these universally distributed superfamilies are compared with genome size in order to estimate the correlation between superfamily duplication and the increase in proteome size. This distinguishes between those size-dependent superfamilies where frequency of occurrence is highly correlated with increase in genome size, and size-independent superfamilies where no correlation is observed. Consideration of the size correlation and the ratio between the mean and the standard deviations for all the superfamily profiles allows more detailed subdivisions and classification of superfamilies. For example, within the size-independent superfamilies, we distinguished a group that are distributed evenly amongst all the genomes. Within the size-dependent superfamilies we differentiated two groups: linearly distributed and non-linearly distributed. Functional annotation using the COG database was performed for all superfamilies in each of these groups, and this revealed significant differences amongst the three sets of superfamilies. Evenly distributed, size-independent domains are shown to be involved primarily in protein translation and biosynthesis. For the size-dependent superfamilies, linearly distributed superfamilies are involved mainly in metabolism, and non-linearly distributed superfamily domains are involved principally in gene regulation.     

Ephemeroptera eggs and their contribution to phylogenetie studies of the order1

Eggs of representative genera of all families of Ephemeroptera except the Palingeniidae were studied. Their external morphology is reviewed, and hypotheses have been proposed to explain the evolution of several chorionic features and types of attachment structure.
The archetypical Ephemeroptera egg is considered to have been round, with a smooth chorion, non-fibrous adhesive layer, funnelform micropyle, and a suprachorionic sperm guide. Subsequent evolution resulted in several different micropyles and many different chorionic sculpturings and attachment structures.
Data obtained from studying the egg stage are utilized as aids to understanding the phytogeny of the Ephemeroptera. The proposed classification divides the order into 21 families arranged into 6 superfamilies.     

Molecular systematics of caridean shrimps based on five nuclear genes: Implications for superfamily classification

Caridean shrimps are the second most diverse group of Decapoda. Over the years, several different systematic classifications, exclusively based on morphology, have been proposed, but the classification of the infraorder Caridea remains unresolved. In this study, five nuclear genes, 18S rRNA, enolase, histone 3, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α-subunit, were used to examine the systematic status of caridean families and superfamilies. We constructed gene trees based on a combined dataset of 3819 bp, containing 35 caridean species from 19 families in 11 superfamilies. At the family level, and based on our restricted representation, our molecular data support monophyly of the families Glyphocrangonidae, Crangonidae, Pandalidae, Alpheidae, Rhynchocinetidae, Nematocarcinidae, Pasiphaeidae, Atyidae and Stylodactylidae. In contrast, both the Hippolytidae and Palaemonidae are polyphyletic in our analysis. Two major clades are revealed. The Alpheidae, Hippolytidae, Crangonidae, Glyphocrangonidae, Barbouriidae, Pandalidae, Hymenoceridae, Gnathophyllidae and Palaemonidae make up the first clade, while the second clade comprises the Rhynchocinetidae, Oplophoridae, Nematocarcinidae, Alvinocarididae, Campylonotidae, Pasiphaeidae and Eugonatonotidae. Two families, Bathypalaemonellidae and Stylodactylidae, are shown to be basal groups in our tree. At the superfamily level, our results do not support the currently accepted superfamily classification, although there is support for a superfamily Palaemonoidea, though only three out of its eight families are included. The results suggest that the currently accepted superfamily classification of the Caridea does not reflect their evolutionary relationships. A major revision of the higher systematics of Caridea appears thus to be vital, ideally incorporating both molecular and morphological evidence.     

A phylogenetic study of the 'bombycoid complex' (Lepidoptera) using five protein-coding nuclear genes, with comments on the problem of macrolepidopteran phylogeny

Abstract This study had two aims. First, we tested the monophyly of and relationships within the ‘bombycoid complex’, an assembly of approximately 5300 species postulated by Minet to represent 12 families in three superfamilies, by sequencing five protein‐coding nuclear gene regions (CAD, DDC, enolase, period, wingless; approximately 6750 bp total) in 66 representatives of most of the subfamilies and tribes. Second, we sought initial evidence on the utility of these genes for estimating relationships among Macrolepidoptera more broadly (11 superfamilies total), by adding representatives of eight families from four other superfamilies, and by assessing the phylogenetic information content of the individual genes and partitions thereof. Analysis of the combined data by likelihood and parsimony upholds monophyly for the bombycoid complex and for Bombycoidea sensu stricto (includes Anthelidae, see below), but with weak bootstrap support. Minet’s assignment of Phiditiinae to Bombycoidea rather than to Noctuoidea is strongly upheld, but Anthelidae, placed in Lasiocampoidea by Minet, group securely within Bombycoidea sensu stricto. Within the latter, the basal split segregates a strongly supported ‘BALE’ group [Apatelodinae + (Eupterotidae + (Brahmaeidae + Lemoniidae))]. The remaining families form a consistently but weakly supported clade, within which the basal split segregates the very strongly supported ‘CAPOPEM’ group [Carthaeidae, Anthelidae, Phiditiinae, (Prismostictini + (Endromidae + (Oberthueriini + Mirinidae)))]. The remaining bombycoids are grouped, very weakly, as Sphingidae + (Bombycinae + Saturniidae). All multiply‐sampled families are strongly recovered, in both outgroups and ingroups, except that Bombycidae sensu Minet are rendered decisively polyphyletic. All genes make important contributions to the combined data results, and there is little strong conflict among genes or between synonymous and nonsynonymous change, although two instances of inter‐gene conflict were notable, one in Lasiocampidae and one in Mimallonidae. Overall, about 75% of nodes are strongly supported (i.e. bootstrap value ≥80%). Superfamilies are recovered, but not always strongly, whereas relationships among superfamilies are recovered only weakly and inconsistently; even within the reasonably well‐sampled Bombycoidea sensu stricto, a (to us) surprising number of interfamily relationships remain uncertain. Thus, it seems clear that substantially more genes, plus additional taxon sampling in most superfamilies, will be required to resolve macrolepidopteran phylogeny.     

Polycladida phylogeny and evolution: integrating evidence from 28S rDNA and morphology

Polyclad flatworms have a troubled classification history, with two contradicting systems in use. They both rely on a ventral adhesive structure to define the suborders Acotylea and Cotylea, but superfamilies were defined according to eyespot arrangement (Prudhoe’s system) or prostatic vesicle characters (Faubel’s system). Molecular data available cover a very limited part of the known polyclad family diversity and have not allowed testing morphology-based classification systems on Polycladida yet. We thus sampled a suitable marker, partial 28S ribosomal DNA (rDNA), from Polycladida (19 families and 32 genera), generating 136 new sequences and the first comprehensive genetic dataset on polyclads. Our maximum likelihood (ML) analyses recovered Polycladida, but the traditional suborders were not monophyletic, as the supposedly acotyleans Cestoplana and Theama were nested within Cotylea; we suggest that these genera should be included in Cotylea. The partial 28S rDNA trees were generally well supported and robust but in conflict with both Faubel’s and Prudhoe’s superfamilies. Therefore, we compiled morphological and anatomical characters for all taxa used and examined their distribution on our molecular tree. Combining morphological and molecular evidence, we redefined polyclad superfamilies. Acotylea contain tentaculated and atentaculated groups and is now divided in three superfamilies. The suborder Cotylea can be divided in five superfamilies. In general, there is a trait of anteriorization of sensory structures, from the plesiomorphic acotylean body plan to the cotylean gross morphology. Traditionally used characters, such as prostatic vesicle, eyespot distribution, and type of pharynx, are all homoplastic and likely have misled polyclad systematics so far.