Towards the phylogeny of the Curculionoidea (Coleoptera): Reconstructions from mitochondrial and nuclear ribosomal DNA sequences

With about 60,000 described species, Curculionoidea represent the most species-rich superfamily in the animal kingdom. The immense diversity apparently creates difficulties in the reconstruction of the phylogenetic relationships. Independent morphological studies have led to very different classifications. This study is based on molecular data from two independent molecular sources, the 16S and 18S rDNA. Sensitivity analyses were conducted for the sequence alignment (gap costs were varied) as well as the phylogenetic reconstruction algorithms and some of their parameters. The higher-level relationships reconstructed within Curculionoidea are sensitive to alignment and reconstruction method. Nemonychidae or Oxycorynidae+Belidae were found to be sister to all remaining Curculionoidea in many analyses. The 16S rDNA sequence data (obtained from 157 species) corroborate many tribes and genera as monophyletic. It is observed that the phylogenetic reconstruction of genera with specific genetic features such as polyploidy and parthenogenetic reproduction is difficult in weevils. The curculionid subfamily Lixinae appears monophyletic. A new monophylum consisting of Entiminae, Hyperinae, Cyclominae, Myllorhinus plus possibly the Cossoninae is distinguished and we call it Entiminae s.l. For most other subfamilies and families homoplasy concealed the phylogenetic signal (due to saturation of the 16S sequences), or the species sampling was insufficient, although our sampling scheme was rather broad. We observed that although data from one source can easily be misleading (16S) or hardly informative (18S), the combination of the two independent data sets can result in useful information for such a speciose group of organisms. Our study represents the most thorough analysis of molecular sequence data of the Curculionoidea to date and although the phylogenetic results appear less stable than expected, they reflect the information content of these sequence data realistically and thus contribute to the total knowledge about the phylogeny of the Curculionoidea.     

Could bacterial associations determine the success of weevil species?

The weevil superfamily Curculionoidea is the largest insect group and so the largest animal group on earth. This taxon includes species which represent an important threat to many economically important crops and, therefore, pose a risk to agriculture and food security. Insect–bacteria associations have been recognised to provide the insect host with many benefits, such as ensuring the acquisition of essential nutrients or protecting the host from natural enemies. The role of bacteria associations within the weevil superfamily remains nonetheless understudied in comparison with other insect taxa. This review draws together existing knowledge on the influence of bacteria associated with weevils known to be agricultural pest species. The implications of these weevil–bacterial associations in determining pest status and their relevance to targeted pest management interventions are discussed. Specific consideration is given to the role of bacteria in cuticle formation, flight activity, reproduction manipulation and adaptation to different environments and food sources.     

Structural diversity of adipokinetic hormones in the hyperdiverse coleopteran Cucujiformia

Seventeen species of the coleopteran series Cucujiformia are investigated for the presence and sequence of putative adipokinetic hormones (AKHs). Cucujiformia includes species from the major superfamilies, that is, Chrysomeloidea, Curculionoidea, Cucujoidea, and Tenebrionoidea. The clade Phytophaga in which the Chrysomeloidea and Curculionoidea reside, harbor very detrimental species for agriculture and forestry. Thus, this study aims not only to demonstrate the structural biodiversity of AKHs in these beetle species and possible evolutionary trends but also to determine whether the AKHs from harmful pest species can be used as lead substances for a future putative insecticide that is harmless to beneficial insects. Sequence analysis of AKHs is achieved by liquid chromatography coupled to mass spectrometry. Most of the investigated species contain AKH octapeptides in their corpora cardiaca, although previously published work also found a few decapeptides, which we comment on. The signature and sole AKH in cerambycidae Chrysomeloidea and Curculionoidea is Peram‐CAH‐I (pEVNFSPNW amide), which is also found in the majority of chrysomelidae Chrysomeloidea and in the one investigated species of Cucujoidea albeit in a few cases associated with a second AKH which can be either Peram‐CAH‐II (pELTFTPNW amide), Emppe‐AKH (pEVNFTPNW amide), or Micvi‐CC (pEINFTPNW amide). The most often encountered AKH in Tenebrionoidea, family Meloidae as well as family Tenebrionidae, is Tenmo‐HrTH (pELNFSPNW amide) followed by Pyrap‐AKH (pELNFTPNW amide) and a Tenmo‐HrTH extended decapeptide (in Meloidae). Finally, we examine AKH sequences from 43 species of cucujiform beetles, including the superfamily Coccinelloidea for a possible lead compound for producing a cucujiform‐specific pesticide.     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Spermatozoa and phylogeny of Curculionoidea (Coleoptera)

In the examined families of Curculionoidea (Coleoptera), the sperm, although characteristic of typical pterygote insects, shows a few peculiarities that suggest Curculionoidea to be a homogeneous group. The curculionid sperm, in fact, always follows a similar structural design, without any variation. For example, it has 2 mitochondrial derivatives of different sizes, the larger of which is almost completely filled with a crystalline protein, the other being more moderately crystallized and almost completely occupied by cristae, and 2 accessory bodies of different sizes that are made up of a crystalline portion, crescent-shaped in section, and a “puff”-like expansion that is of different consistency, shape, and symmetry in various cases. The different extensions of the accessory bodies seem, therefore, to compensate for the high degree of asymmetry due to the largely different sizes of the 2 mitochondrial derivatives.The examined families and subfamilies can be arranged in 2 groups: Rhynchitidae appear drastically isolated, because they have a peculiar “9 + 9 + 0” axoneme, and show, moreover, a limited degree of asymmetry in the tail organelles. The remaining families and subfamilies are more closely related to one another by the presence of a “9 + 9 + 2” classical axoneme and by the same degree of asymmetry in the tail, typical of curculionid sperm. Among them, Apionidae are distinguished for the space containing the extraacrosomal layer, which may be hollow or absent, a twice-stepped nucleus-tail connection, and a thick glycocalyx at the end of the tail.The Curculionidae conserve primitive characters, such as the 3-layered acrosomal complex and “9 + 9 + 2” axoneme, but also present a high degree of differentiation in the shape of the asymmetrical tail organelles. There appear to be 3 clusters: the first cluster includes Brachyderinae, Leptopiinae, Gymnetrinae, Cryptorhynchinae, Rhynchophorinae. The second cluster includes Scolytidae, Cleoninae, Hylobiinae. The third cluster is more numerous and heterogeneous and shows 3 subgroups. The first of these includes only Otiorhynchinae. The sum of their characters shows that they have most of the common features of primitive curculionids; however the differences between a genus and another are so large that they could be assigned to different subfamilies. The second subgroup includes Hyperinae, Pissodinae, Magdalinae, Ceutorhynchinae and Cossoninae, and the third group includes Cioninae, Anthonominae, and Barimae.It is difficult to arrange these subfamilies (frequently recognizable for a different combination of the same recurrent characters) in a phylogenetic tree. However, we observed signs of primitiveness in Brachyderinae (small crescents) and their cluster; advanced ones in the third and fourth clusters all evolved with different patterns of the puff-like expansion of one of the accessory bodies, the latter being the most peculiar character of the superfamily. A tentative reconstruction is given.The functional significance of the variations seems to be that Rhynchitidae seem to be evolving towards immotility (their spermatozoon, in fact, is able to produce only a series of vibrations, not the progressive series of waves as in all other species studied), while all the other families and subfamilies show no signs of alterations in axonemal pattern and motility. The main evolutionary pathways observed in them are towards compensating for an exaggerated lengthening and a greater degree of asymmetry in the tail organelles: one of them, the major mitochondrial derivative, acts as a rigid axis, while the axoneme produces undulations in the opposite portion of the axonemal section.     

Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia)

A large‐scale phylogenetic study is presented for Cucujoidea (Coleoptera), a diverse superfamily of beetles that historically has been taxonomically difficult. This study is the most comprehensive analysis of cucujoid taxa to date, with DNA sequence data sampled from eight genes (four nuclear, four mitochondrial) for 384 coleopteran taxa, including exemplars of 35 (of 37) families and 289 genera of Cucujoidea. Maximum‐likelihood analyses of these data present many significant relationships, some proposed previously and some novel. Tenebrionoidea and Lymexyloidea are recovered together and Cleroidea forms the sister group to this clade. Chrysomeloidea and Curculionoidea are recovered as sister taxa and this clade (Phytophaga) forms the sister group to the core Cucujoidea (Cucujoidea s.n .). The nitidulid series is recovered as the earliest‐diverging core cucujoid lineage, although the earliest divergences among core Cucujoidea are only weakly supported. The cerylonid series (CS) is recovered as monophyletic and is supported as a major Cucujiform clade, sister group to the remaining superfamilies of Cucujiformia. Currently recognized taxa that were not recovered as monophyletic include Cucujoidea, Endomychidae, Cerylonidae and Bothrideridae. Biphyllidae and Byturidae were recovered in Cleroidea. The remaining Cucujoidea were recovered in two disparate major clades: one comprising the nitidulid series + erotylid series + Boganiidae and Hobartiidae + cucujid series, and the other comprising the cerylonid series. Propalticidae are recovered within Laemophloeidae. The cerylonid series includes two major clades, the bothriderid group and the coccinellid group. Akalyptoischiidae are recovered as a separate clade from Latridiidae. Eupsilobiinae are recovered as the sister taxon to Coccinellidae. In light of these findings, many formal changes to cucujiform beetle classification are proposed. Biphyllidae and Byturidae are transferred to Cleroidea. The cerylonid series is formally recognized as a new superfamily, Coccinelloidea stat.n. Current subfamilies elevated (or re‐elevated) to family status include: Murmidiidae stat.n. , Teredidae stat.n. , Euxestidae stat.n. , Anamorphidae stat.rev. , Eupsilobiidae stat.n. , and Mycetaeidae stat.n. The following taxa are redefined and characterized: Cleroidea s.n. , Cucujoidea s.n. , Cerylonidae s.n. , Bothrideridae s.n. , Endomychidae s.n. A new subfamily, Cyclotominae stat.n. , is described. Stenotarsinae syn.n. is formally subsumed within a new concept of Endomychinae s.n.     

Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes

Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation.     

Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily.

A comprehensive, structural and functional, in silico analysis of the medium-chain dehydrogenase/reductase (MDR) superfamily, including 583 proteins, was carried out by use of extensive database mining and the blastp program in an iterative manner to identify all known members of the superfamily. Based on phylogenetic, sequence, and functional similarities, the protein members of the MDR superfamily were classified into three different taxonomic categories: (a) subfamilies, consisting of a closed group containing a set of ideally orthologous proteins that perform the same function; (b) families, each comprising a cluster of monophyletic subfamilies that possess significant sequence identity among them and might share or not common substrates or mechanisms of reaction; and (c) macrofamilies, each comprising a cluster of monophyletic protein families with protein members from the three domains of life, which includes at least one subfamily member that displays activity related to a very ancient metabolic pathway. In this context, a superfamily is a group of homologous protein families (and/or macrofamilies) with monophyletic origin that shares at least a barely detectable sequence similarity, but showing the same 3D fold. The MDR superfamily encloses three macrofamilies, with eight families and 49 subfamilies. These subfamilies exhibit great functional diversity including noncatalytic members with different subcellular, phylogenetic, and species distributions. This results from constant enzymogenesis and proteinogenesis within each kingdom, and highlights the huge plasticity that MDR superfamily members possess. Thus, through evolution a great number of taxa-specific new functions were acquired by MDRs. The generation of new functions fulfilled by proteins, can be considered as the essence of protein evolution. The mechanisms of protein evolution inside MDR are not constrained to conserve substrate specificity and/or chemistry of catalysis. In consequence, MDR functional diversity is more complex than sequence diversity. MDR is a very ancient protein superfamily that existed in the last universal common ancestor. It had at least two (and probably three) different ancestral activities related to formaldehyde metabolism and alcoholic fermentation. Eukaryotic members of this superfamily are more related to bacterial than to archaeal members; horizontal gene transfer among the domains of life appears to be a rare event in modern organisms.     

Trophic associations and specialization of phytophagous beetles (Coleoptera: Chrysomeloidea,Curculionoidea) in the east of the Russian Plain

Data on the trophic associations of beetles with plants in the east of the Russian Plain are summarized and comparative analysis of host specialization of different groups of phytophagous beetles is performed. In terms of the width of the regional trophic spectrum, monophages and narrow oligophages prevail among the Curculionoidea as a whole and in the families Curculionidae and Apionidae in particular, while moderate and broad oligophages prevail in the Chrysomeloidea and in the family Chrysomelidae. Two-thirds of the regional fauna (66%) of Curculionoidea are closely associated with plants of one genus; by contrast, in Chrysomeloidea almost 40% of the species can develop on plants from different genera of one family, the fraction of the narrowly specialized forms comprising only 43%. The higher level of trophic specialization of weevils (Curculionidae, Apionidae) and seed beetles (Bruchidae), as compared to leaf beetles (Chrysomelidae), is probably due to the larval endophagy of most species of these families. Analysis of the distribution of beetles over host plants has shown that the specialized forms are associated with plants of 65 families (about 60% of the regional flora in the east of the Russian Plain). Distribution of beetles over plant families is very non-uniform. Most of the specialized forms (78%) are associated with plants of 15 families, three of which (Asteraceae, Fabaceae, and Brassicaceae) include hosts of more than onethird of the beetle species (37%). Monophages and narrow oligophages are recorded on 201 genera of plants from 59 families. Polyphagous species are recorded on plants of 58 families. The specific features of the distribution of phytophagous beetles over host plants (as compared to other insects) is a high fraction of species developing on coenophobes (particularly those of the family Brassicaceae) typical of the pioneer stages of successions with sparse herbaceous cover, and a small number of species associated with grasses and sedges. These features are most conspicuous in the fauna of Curculionidae.     

Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea)

We performed a comparative study of partial rDNA sequences from a variety of Coleoptera taxa to construct an annotated alignment based on secondary structure information, which in turn, provides improved rRNA structure models useful for phylogenetic reconstruction. Subsequent phylogenetic analysis was performed to test monophyly and interfamilial relationships of the megadiverse plant feeding beetle group known as ‘Phytophaga’ (Curculionoidea and Chrysomeloidea), as well as to discover their closest relatives among the Cucujiformia. Parsimony and Bayesian analyses were performed based on the structural alignment of segments of 18S rRNA (variable regions V4‐V5, V7‐V9) and 28S rRNA (expansion segment D2). A total of 104 terminal taxa of Coleoptera were included: 96 species of Cucujiformia beetles, representing the families and most ‘subfamilies’ of weevils and chrysomeloids (Phytophaga), as well as several families of Cleroidea, Tenebrionoidea and Cucujoidea, and eight outgroups from three other polyphagan series: Scarabaeiformia, Elateriformia and Bostrichiformia. The results from the different methods of analysis agree — recovering the monophyly of the ‘Phytophaga’, including Curculionoidea and Chrysomeloidea as sister groups. The curculionoid and chrysomeloid phylogeny recovered from the aligned 18S and 28S rDNA segments, which is independent of morphological data, is in agreement with recent hypotheses or concepts based on morphological evidence, particularly with respect to familial relationships. Our results provide clues about the evolutionary origin of the phytophagan beetles within the megaclade Cucujiformia, suggesting that the sister group of ‘Curculionoidea + Chrysomeloidea’ is a clade of the ‘Cucujoidea’, represented in this study by species in Boganiidae, Erotylidae, Nitidulidae, Cucujidae and Silvanidae. The Coccinellidae and Endomychidae are not grouped with the latter, and the remaining terminal taxa are nested in Tenebrionoidea and Cleroidea. We propose that the combination of structurally aligned ribosomal RNA gene regions 18S (V4‐V5, V7‐V9) and 28S (D2) are useful in testing monophyly and resolving relationships among beetle superfamilies and families.     

Rounding up the usual suspects: a standard target‐gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb‐weaving spiders with a new family‐rank classification (Araneae,Araneoidea)

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb‐weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb‐web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb‐web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb‐webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n. ). Araneoidea includes 17 families with the following changes: Araneidae is re‐circumscribed to include nephilines , Nephilinae rank res., Arkyidae rank n. , Physoglenidae rank n. , Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae ( syn. n. ), Holarchaeidae of Anapidae ( syn. n. ) and Sinopimoidae of Linyphiidae ( syn. n. ).     

小蠹亚科的分类地位(鞘翅目,象虫科)

许多学者将小蠹作为象虫总科Curculionoidea中一个独立的科Scolytidae,而目前国际上普遍认为小蠹为象虫科Curculionidae中的一个亚科,即小蠹亚科Scolytinae。Erichson在1842年即提出了小蠹为象虫科的一个亚科,20世纪以R.A.Crowson为代表的学者对此观点表示支持并进行了较为严谨的科学论证,而以S.L.Wood为代表的另外一些学者则坚持小蠹的科级地位,我国学者蔡邦华、殷惠芬等一直沿用该分类系统。近20年来,国际上许多学者通过对小蠹类昆虫的成虫和幼虫外部特征的深入研究,以及支序系统学和分子生物学等一些最新结果,普遍认为小蠹类昆虫应为象虫科的一个亚科,这一观点已被国际上广泛接受。本文全面介绍了小蠹分类研究的历史及新的研究进展,并提出和建议采用"小蠹亚科"这一分类地位,与象虫亚科并列,均隶属于象虫科。     

Phylogenetic distribution of cysteine proteinases in beetles: evidence for an evolutionary shift to an alkaline digestive strategy in Cerambycidae

We characterized the digestive proteinases of eight species of beetles to improve our understanding of the phylogenetic distribution of serine and cysteine proteinases. Serine proteinases function optimally under alkaline pH conditions, whereas cysteine proteinases require acidic pH. The phylogenetic distribution of cysteine proteinases suggests that they first appeared in an early cucujiform ancestor, however, data for some groups is patchy, and there has been speculation that they have been lost in at least one group, the long-horned beetles (Cerambycidae). The pattern we found supports the hypothesized origin of the proteinases and extends their distribution to an additional superfamily. In addition, we confirmed the presence of cysteine proteinases in some Curculionoidea. Cysteine proteinases were absent, however, from all three species of cerambycids surveyed, supporting the hypothesis that this group has reverted to the more ancestral serine (alkaline) digestive strategy. In four species we compared the pH optima for total proteolytic activity to the actual pH of the midgut and found the match between optimal and actual pH to be weaker in the cerambycids. These findings suggest that either a close correlation between midgut pH and the proteolytic pH optimum is not needed for adequate digestive efficiency, or that midgut pH is a more constrained digestive feature and there has been insufficient time for it to shift upwards to maximize serine proteinase activity.     

淡水豚类线粒体DNA 12S rRNA基因的序列变异及其分子系统学研究

淡水豚类４个代表属「白暨豚（Ｌｉｐｏｔｅｓ）、恒河豚（Ｐｌａｔａｎｉｓｔａ）、弗西豚（Ｐｏｎｔｏｐｏｒｉａ）和亚河豚（Ｉｎｉａ）」ｍｔＤＮＡ １２Ｓ ｒＲＮＡ基因的序列差异水平,高于其他齿鲸类科间的差异,特别是远远高于海豚总科内的科间差异。研究结果支持它们应归属于不同的科,即白暨豚科（Ｌｉｐｏｔｉｉｄａｅ）、恒河豚科（Ｐｌａｔａｎｉｓｔｉｄａｅ）、弗西豚科（Ｐｏｎｔｏｐｏｒｉｄａｅ）和亚河豚科（Ｉ     

GHKL, an emergent ATPase/kinase superfamily

An interesting recent development is the recognition of a novel ATP-binding superfamily that includes diverse protein families such as DNA topoisomerase II, molecular chaperones Hsp90, DNA-mismatch-repair enzymes MutL and histidine kinases. The most singular unifying feature of this superfamily is the unconventional Bergerat ATP-binding fold. The far-reaching significance of this commonality is still in the process of being explored.     

The Zn-peptidase superfamily: functional convergence after evolutionary divergence.

Zn-dependent carboxypeptidases (ZnCP) cleave off the C-terminal amino acid residues from proteins and peptides. Here we describe a superfamily that unites classical ZnCP with other enzymes, most of which are known (or likely) to participate in metal-dependent peptide bond cleavage, but not necessarily in polypeptide substrates. It is demonstrated that aspartoacylase (ASP gene) and succinylglutamate desuccinylase (ASTE gene) are members of the ZnCP family. The Zn-binding site along with the structural core of the protein is shown to be conserved between ZnCP and another large family of hydrolases that includes mostly aminopeptidases (ZnAP). Both families (ZnCP and ZnAP) include not only proteases but also enzymes that perform N-deacylation, and enzymes that catalyze N-desuccinylation of amino acids. This is a result of functional convergence that apparently occurred after the divergence of the two families.     

beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases

Comparison of the amino acid sequences of four families of glycosyl hydrolases reveals that they are homologous and have several common conserved regions. Two of these families contain beta-fructosidases (glycosyl hydrolase families GH32 and GH68) and the other two include alpha-L-arabinases and beta-xylosidases (families GH43 and GH62). The latter two families are proposed to be grouped together with the former two into the beta-fructosidase (furanosidase) superfamily. Several ORFs can be considered as a fifth family of the superfamily on the basis of sequence similarity. It is shown for the first time that a glycosyl hydrolase superfamily can include enzymes with both inversion and retention mechanism of action. Composition of the active center for enzymes of the superfamily is discussed.     

Bioinformatics of the TULIP domain superfamily

Proteins of the BPI (bactericidal/permeability-increasing protein)-like family contain either one or two tandem copies of a fold that usually provides a tubular cavity for the binding of lipids. Bioinformatic analyses show that, in addition to its known members, which include BPI, LBP [LPS (lipopolysaccharide)-binding protein)], CETP (cholesteryl ester-transfer protein), PLTP (phospholipid-transfer protein) and PLUNC (palate, lung and nasal epithelium clone) protein, this family also includes other, more divergent groups containing hypothetical proteins from fungi, nematodes and deep-branching unicellular eukaryotes. More distantly, BPI-like proteins are related to a family of arthropod proteins that includes hormone-binding proteins (Takeout-like; previously described to adopt a BPI-like fold), allergens and several groups of uncharacterized proteins. At even greater evolutionary distance, BPI-like proteins are homologous with the SMP (synaptotagmin-like, mitochondrial and lipid-binding protein) domains, which are found in proteins associated with eukaryotic membrane processes. In particular, SMP domain-containing proteins of yeast form the ERMES [ER (endoplasmic reticulum)-mitochondria encounter structure], required for efficient phospholipid exchange between these organelles. This suggests that SMP domains themselves bind lipids and mediate their exchange between heterologous membranes. The most distant group of homologues we detected consists of uncharacterized animal proteins annotated as TM (transmembrane) 24. We propose to group these families together into one superfamily that we term as the TULIP (tubular lipid-binding) domain superfamily.     

Three monophyletic superfamilies account for the majority of the known glycosyltransferases

Sixty-five families of glycosyltransferases (EC 2.4.x.y) have been recognized on the basis of high-sequence similarity to a founding member with experimentally demonstrated enzymatic activity. Although distant sequence relationships between some of these families have been reported, the natural history of glycosyltransferases is poorly understood. We used iterative searches of sequence databases, motif extraction, structural comparison, and analysis of completely sequenced genomes to track the origins of modern-type glycosyltransferases. We show that >75% of recognized glycosyltransferase families belong to one of only three monophyletic superfamilies of proteins, namely, (1) a recently described GPGTF/GT-B superfamily; (2) a nucleoside-diphosphosugar transferase (GT-A) superfamily, which is characterized by a DxD sequence signature and also includes nucleotidyltransferases; and (3) a GT-C superfamily of integral membrane glycosyltransferases with a modified DxD signature in the first extracellular loop. Several developmental regulators in Metazoans, including Fringe and Egghead homologs, belong to the second superfamily. Interestingly, Tout-velu/Exostosin family of developmental proteins found in all multicellular eukaryotes, contains separate domains belonging to the first and the second superfamilies, explaining multiple glycosyltransferase activities in one protein.     

蜡蝉总科(昆虫纲:半翅目)系统分类研究进展

蜡蝉总科隶属于半翅目头喙亚目,大致可分为18～21个科。中国记载16科。蜡蝉总科的科级系统发育关系一直存在着广泛争议,至今尚无一个为大多数学者所接受的分类系统。因此,研究蜡蝉总科的系统发育具有重要的理论价值。本文从种及种下阶元的分类鉴定、种上阶元的系统发育、生物地理学等方面对蜡蝉总科的分类研究进行综述。