Revision of the superfamily Rhynchoporoidae Muir-Wood, 1955

The revision of punctate rhynchonellids of the superfamily Rhynchoporoidea revealed that the superfamily is composite. Based on the detail study of shell interior, the punctate rhynchonellids of the genus Rhynchopora King, 1865, subfamily Rhynchoporinae Muir-Wood, 1955 are placed into the family Trigonirhynchiidae Schmidt, 1965, superfamily Rhynchotrematoidea Schuchert, 1913. The genera Greira Erlanger, 1993, Tchanakhtchirostrum Sartenaer et Plodowski, 2003, Sharovaella Pakhnevich, 2012, Zaigunrostrum Sartenaer et Plodowski, 2003 are also referred to this family within the subfamily Greirinae Erlanger, 1993. The only genus of the subfamily Tretorhynchinae Savage, 2002, Tretorhynchia Brunton, 1971, is moved to the family Leiorhynchidae Stainbrook, 1945, superfamily Camarotoechioidea Schuchert, 1929. Araratella Abrahamian, Plodowski, et Sartenaer, 1975 within the subfamily Araratellinae Erlanger, 1986 is referred to the family Septalariidae Havlicek, 1960 of the same superfamily. The position of Rariella Zhang, 1981, Yingtangella Bai et Ying, 1977, Momarhynchus Baranov et Sartenaer, 1996 in the order Rhynchonellida remains controversial. The punctation and exopunctation is found to arise parallel in different rhynchonellid evolutionary branches after the Frasnian-Famennian mass extinction.     

Systematic position and composition of the superfamily Notanoplioidea Gill, 1969 (Brachiopoda, Articulata)

The systematic position of several genera of articulate brachiopods grouped around Notanoplia Gill is controversial. Notanoplia was established in 1950 within the order Chonetida; this genus and several externally similar genera, which were established later, were referred by different authors to the orders Orthida, Strophomenida, Chonetida, Atrypida, Spiriferida, or considered as incertae sedis. The morphological analysis of the shell of Notanoplia and the related genera Boucotia and Costanoplia supports the placement of these genera in a separate superfamily, Notanoplioidea, within the order Strophomenida. Other genera similar in the shell outline and shape to Notanoplia and conditionally considered as related to it probably belong to other strophomenid superfamilies or other orders.     

The position of the genus Heterotropus in the system of Brachycera-Orthorrhapha (Diptera)

The position of the genus Heterotropus Loew is considered based on the data on biology of Heterotropus ammophilus Paramonov. Judging by the larval morphology and biology, the subfamily Heterotropinae should be elevated to the family rank and considered within the superfamily Bombylioidea, together with Bombyliidae, Nemestrinidae, and Apioceridae.     

Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases

Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the α-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.     

Taxonomie und Systematik der HippocardioideaPojeta & Runnegar, 1976 [n. superfam.] (Mollusca; Rostroconchia)

The revisions of the families PseudobigaleaidaeHoare, Mapes &; Yancey, 2002 and HippocardiidaePojeta &; Runnegar, 1976 led to the introduction of a new taxon at the superfamily rank in order to unite the two families and distinguish them from the members of the Conocardiidae and Bransoniidae within the order Conocardiida. The autapomorphy of this new superfamily HippocardioideaPojeta &; Runnegar, 1976 [n. superfam.] — the more or less uniform development of at least one hood — is considered taxonomically as so important that we exclude a common ancestry of the almost contemporaneously occurring taxa of the Hippocardiidae, Pseudobigaleaidae on the one hand and the Bransoniidae sensuPojeta &; Runnegar on the other. The family Hippocardiidae is divided into six taxa on subfamily rank, the HippocardiinaePojeta &; Runnegar, Babinicardiinae n. subfam., Barrandeicardiinae n. subfam., Bohemicardiinae n. subfam., Goticardiinae n. subfam. and Hassiacardiinae n. subfam. At the species level, 13 taxa are assigned to the generaBabinicardia n. gen.,Barrandeicardia n. gen.,Bohemicardia n. gen.,Filicardia n. gen,.Globocardia n. gen.,Goticardia n. gen.,Pohlia n. gen. andHassiacardia n. gen. Additionally, the speciesGoticardia kauffmannii n. gen. n. sp. is introduced, whereas the primary homonymy of ?Conocardium“reticulatum Babin, 1966 is retained, because this taxon remained inassignable to any of the existing genera, but is considered as a member of the Hippocardiidae. The revised family Hippocardiidae occurred stratigraphically from the Middle Silurian (Wenlockian) until Mississippian time; members of the new superfamily Hippocardioidea are known from the Ordovician until the Pennsylvanian.     

A reclassification of the millipede superfamily Trichopolydesmoidea,with descriptions of two new species from the Aegean region (Diplopoda,Polydesmida)

Two new species are described from caves in several Greek islands in the Aegean Sea: Galliocookia gracilis sp. n., a presumed troglobite from Rhodes, Dodecanese Islands, and Sphaeroparia simplex sp. n., likely a troglophile from Kithnos, Cyclades, and Chios, Eastern Sporades. These genera are assigned to the family Trichopolydesmidae Verhoeff, 1910. Because Sphaeroparia Attems, 1909, an Afrotropical genus, nicely bridges the gap, both morphologically and geographically, between the Euro-Mediterranean Trichopolydesmidae and the much more diverse, pantropical Fuhrmannodesmidae Brölemann, 1916, the latter family is considered as a new junior subjective synonym of the former, syn. n. Thus expanded, the family Trichopolydesmidae is rediagnosed and its position within the superfamily Trichopolydesmoidea refined. Because the families Mastigonodesmidae Attems, 1914, Macrosternodesmidae Brölemann, 1916 and Nearctodesmidae Chamberlin & Hoffman, 1950 are also formally synonymized with Trichopolydesmidae, syn. n., the Trichopolydesmoidea currently contains only two families, Trichopolydesmidae and Opisotretidae Hoffman, 1980.     

Shell microstructure and variability of cell imprints of the mantle outer epithelium in the genus <Emphasis Type="Italic">Suiaella</Emphasis> Moisseev (Brachiopoda,Rhynchonellida) from the Lower Cretaceous of Crimea

The shell microstructure of the Lower Cretaceous Suiaella weberi Moisseev, 1949 (superfamily Norelloidea) from the Lower Barremian of Crimea is studied for the first time. The fibers of Suiaella are shown to differ strongly in size and outline of cross section from the fibers of the superfamily Rhynchonelloidea. Suiaella is shown to differ from rhynchonellids of the superfamily Basilioloidea in the presence of straight or slightly curved fibers and absence of twisted fibers and overlapping adjacent fibers within one and the same bundle, it also differs in the presence of capillation and fine ribbing. Numerous cell imprints of the mantle outer epithelium have been found in fossil Norelloidea for the first time.     

Mutations in a Conserved Domain of E. coli MscS to the Most Conserved Superfamily Residue Leads to Kinetic Changes

In Escherichia coli (E. coli) the mechanosensitive channel of small conductance, MscS, gates in response to membrane tension created from acute external hypoosmotic shock, thus rescuing the bacterium from cell lysis. E. coli MscS is the most well studied member of the MscS superfamily of channels, whose members are found throughout the bacterial and plant kingdoms. Homology to the pore lining helix and upper vestibule domain of E. coli MscS is required for inclusion into the superfamily. Although highly conserved, in the second half of the pore lining helix (TM3B), E. coli MscS has five residues significantly different from other members of the superfamily. In superfamilies such as this, it remains unclear why variations within such a homologous region occur: is it tolerance of alternate residues, or does it define functional variance within the superfamily? Point mutations (S114I/T, L118F, A120S, L123F, F127E/K/T) and patch clamp electrophysiology were used to study the effect of changing these residues in E. coli MscS on sensitivity and gating. The data indicate that variation at these locations do not consistently lead to wildtype channel phenotypes, nor do they define large changes in mechanosensation, but often appear to effect changes in the E. coli MscS channel gating kinetics.     

Evolution of quinol oxidation within the heme‑copper oxidoreductase superfamily

The heme?copper oxidoreductase (HCO) superfamily is a large superfamily of terminal respiratory enzymes that are widely distributed across the three domains of life. The superfamily includes biochemically diverse oxygen reductases and nitric oxide reductases that are pivotal in the pathways of aerobic respiration and denitrification. The adaptation of HCOs to use quinol as the electron donor instead of cytochrome c has significant implication for the respiratory flexibility and energetic efficiency of the respiratory chains that include them. In this work, we explore the adaptation of this scaffold to two different electron donors, cytochromes c and quinols, with extensive sequence analysis of these enzymes from publicly available datasets. Our work shows that quinol oxidation evolved independently within the HCO superfamily at least seven times. Enzymes from only two of these independently evolved clades have been biochemically well-characterized. Combining structural modeling with sequence analysis, we identify putative quinol binding sites in each of the novel quinol oxidases. Our analysis of experimental and modeling data suggests that the quinol binding site appears to have evolved at the same structural position within the scaffold more than once.     

Crystal Structure of the Ectoine Hydroxylase,a Snapshot of the Active Site

Ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. They also serve as chemical chaperones and maintain the functionality of macromolecules. 5-Hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (EctD). The EctD protein is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily and is evolutionarily well conserved. We studied the ectoine hydroxylase from the cold-adapted marine ultra-microbacterium Sphingopyxis alaskensis (Sa) and found that the purified SaEctD protein is a homodimer in solution. We determined the SaEctD crystal structure in its apo-form, complexed with the iron catalyst, and in a form that contained iron, the co-substrate 2-oxoglutarate, and the reaction product of EctD, 5-hydroxyectoine. The iron and 2-oxoglutarate ligands are bound within the EctD active site in a fashion similar to that found in other members of the dioxygenase superfamily. 5-Hydroxyectoine, however, is coordinated by EctD in manner different from that found in high affinity solute receptor proteins operating in conjunction with microbial import systems for ectoines. Our crystallographic analysis provides a detailed view into the active site of the ectoine hydroxylase and exposes an intricate network of interactions between the enzyme and its ligands that collectively ensure the hydroxylation of the ectoine substrate in a position- and stereo-specific manner.     

On the systematics of some marine haploporids (Trematoda) with the description of a new species of Megasolena Linton, 1910

Megasolena mikra sp. nov. is described from the queen angelfish, Holacanthus ciliaris (Linnaeus), off Florida, USA. The new species can be differentiated from all other species of Megasolena Linton, 1910 except Megasolena littoralis Muñoz, George-Nascimento, and Bray, 2017 in possessing testes that are smaller in diameter than the ovary. The new species can be differentiated from M. littoralis in lacking tegumental spines and possessing oral sucker papillae. Molecular data are provided for two species each of Cadenatella Dollfus, 1946, Hapladena Linton, 1910, and Megasolena Linton, 1910. Bayesian inference analysis of concatenated internal transcribed spacer region-2 (ITS2) and partial 28S rDNA sequences of 50 haploporoids revealed 1) a monophyletic Atractotrematidae Yamaguti, 1939 sister to the rest of the haploporoids tested; 2) a paraphyletic Megasoleninae Manter, 1935 – if Hapladena is included; and 3) a monophyletic Cadenatellinae Gibson and Bray, 1982 sister to the ‘mugilid’ haploporids. The ‘mugilid’ haploporids formed a monophyletic clade consisting of the subfamilies Chalcinotrematinae Overstreet and Curran, 2005, Forticulcitinae Blasco-Costa, Balbuena, Kostadinova, and Olson, 2009, Haploporinae Nicoll, 1914, and Waretrematinae Srivastava, 1937. Based on our analysis we restrict the Megasoleninae to include Megasolena, Vitellibaculum Montgomery, 1957, and Metamegasolena Yamaguti, 1970, all of which have species with two testes. To accommodate the former megasolenine taxa with a single testis, we erect the Hapladeninae subf. nov. for species in Hapladena and tentatively, Myodera Montgomery, 1957. Our results further support that haploporoids had a common marine ancestor with two testes, and that members of the Haploporoidea Nicoll, 1914 underwent diversification following a shift from a primarily marine life history with eupercarian hosts to a more euryhaline one with diadromous hosts (namely mullet).     

The beetle-like Palaeozoic and Mesozoic roachoids of the so-called “umenocoleoid” lineage (Dictyoptera: Ponopterixidae fam. nov.)

The position of Palaeozoic and Mesozoic roachoids and their relationships to crown-group Dictyoptera is an unresolved problem of insect systematics since Hennig's time. This contribution presents new data based on the wing venation of the Early Cretaceous group Cratovitismioidea (so-called “Umenocoleoidea”) supplemented with the discovery of the first Late Palaeozoic representative. As Umenocoleus, type genus of the Umenocoleidae, is considered as a Coleopterida, the roachoids currently included in the Umenocoleidae are transferred to the new family Ponopterixidae, in the new superfamily Cratovitismioidea. Permoponopterix lodevensis, a new ponopterixid genus and species, is described as the oldest representative of this superfamily, from the Middle Permian of the South of France. A new species Ponopterix burkhardi is described from the Lower Cretaceous of Crato Formation in Brazil. Convergent adaptations of tegmina in Coleopterida, Protelytroptera and Cratovitismioidea are discussed.     

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes

Background

The availability of complete genome sequences enables all the members of a gene family to be identified without limitations imposed by temporal, spatial or quantitative aspects of mRNA expression. Using the nearly completed human genome sequence, we combined in silico and experimental approaches to define the complete human nuclear receptor (NR) set. This information was used to carry out a comparative genomic study of the NR superfamily.

Results

Our analysis of the human genome identified two novel NR sequences. Both these contained stop codons within the coding regions, indicating that both are pseudogenes. One (HNF4 γ-related) contained no introns and expressed no detectable mRNA, whereas the other (FXR-related) produced mRNA at relatively high levels in testis. If translated, the latter is predicted to encode a short, non-functional protein. Our analysis indicates that there are fewer than 50 functional human NRs, dramatically fewer than in Caenorhabditis elegans and about twice as many as in Drosophila. Using the complete human NR set we made comparisons with the NR sets of C. elegans and Drosophila. Searches for the >200 NRs unique to C. elegans revealed no human homologs. The comparative analysis also revealed a Drosophila member of NR subfamily NR3, confirming an ancient metazoan origin for this subfamily.

Conclusions

This work provides the basis for new insights into the evolution and functional relationships of NR superfamily members.     

Musculature of the male genitalia of Xylophagus cinctus (De Geer) and relationships within the superfamily Xylophagoidea (Diptera, Brachycera)

There is no general agreement on relationships within Xylophagoidea (Diptera, Brachycera). The musculature of the male genitalia of Xylophagus cinctus (De Geer) (Xylophagidae, the most primitive family of Brachycera) is described and compared with that of some other Xylophagoidea: Exeretonevridae (Exeretonevra angustifrons Hardy), Coenomyiidae (Anacanthaspis biafasciata Röder), and Rhagionidae (Rhagio montanus Becker, Chrysopilus dives Loew, and Ch. helvolus Meigen) discussed earlier (Ovtshinnikova, 1989, 1998; Palmer et al., 2000). In spite of the differences in the structure of the genital sclerites, Xylophagidae possess all the muscles found in Coenomyiidae and Rhagionidae. The musculature of the male genitalia of Xylophagus cinctus includes two muscle pairs of the aedeagus sheath (M1 and M2); three muscle pairs of the ejaculatory complex (M30, M31, and M32); one muscle pair of the gonocoxites (M33); two muscle pairs of the gonostyli (M27 and M28); one muscle pair of the proctiger (M21), one muscle pair of the cerci (M29); two pairs of the tergosternal muscles (M5 ¹ and M5 ²); and two pairs of the pregenital muscles (M18 and M19). Muscles of the family Exeretonevridae are mostly the same, except for the muscles of the cerci M29, proctiger M29, and pregenital muscles M18 and M19, that are subdivided into two parts. This fact and also a different degree of the development of muscles M32 and M5 ² clearly distinguish Exeretonevridae from closely related families. The attachment places of the muscles of the aedeagus sheath M2 and of the gonostyli M28, as well as the split character of the tergosternal muscle pair M5 ¹ makes it possible to distinguish two sister groups, Xylophagidae plus Exeretonevridae, versus Coenomyiidae plus Rhagionidae. It should be noted that the muscles of the male genitalia of Xylophagidae, Exeretonevridae, Coenomyiidae, and Rhagionidae possess similar plesiomorphic characters, and these families should be united into the superfamily Xylophagoidea. This superfamily is the most primitive superfamily of Brachycera Orthorrhapha and possesses the most stable set and arrangement of male genital muscles within the entire suborder. An improved dendrogram of the phylogenetic relationships between the known groups of Xylophagoidea is proposed on the basis of the structure of male genital muscles.     

TRI12, a trichothecene efflux pump from Fusarium sporotrichioides: gene isolation and expression in yeast

Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster. Here we report the complete sequence for TRI12, a gene encoding a trichothecene efflux pump that is located within the trichothecene gene cluster of F. sporotrichioides. TRI12 encodes a putative polypeptide of 598 residues with sequence similarities to members of the major facilitator superfamily (MFS) and is predicted to contain 14 transmembrane-spanning segments. Disruption of TRI12 results in both reduced growth on complex media and reduced levels of trichothecene production. Growth of tri12 mutants on trichothecene-containing media is inhibited, suggesting that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes. Functional analysis of TRI12 was performed by expressing it in yeast strains that were co-transformed with a gene (TRI3) encoding a trichothecene 15-O-acetyltransferase. In the presence of the TRI3 substrate, 15-decalonectrin, cultures of yeast strains carrying TRI12 and TRI3 accumulated much higher levels of the acetylated product, calonectrin, than was observed for strains carrying TRI3 alone. PDR5, a transporter of the ABC superfamily, which is known to mediate trichothecene resistance in yeast, increased calonectrin accumulation in TRI12/TRI3 yeast strains but not in TRI3 strains. These results confirm the involvement of TRI12 in the trichothecene efflux associated with toxin biosynthesis, and demonstrate the usefulness of yeast as a host system for studies of MFS-type transporters.     

Vitellogenesis of the digenean Plagiorchis elegans (Rudolphi, 1802) (Plagiorchioidea,Plagiorchiidae)

The ultrastructural organization of vitellogenesis of Plagiorchis elegans (Rudolphi, 1802), experimentally obtained from the golden hamster Mesocricetus auratus (Linnaeus, 1758), is described using transmission electron microscopy. This study is the first ultrastructural study of vitellogenesis in a member of the superfamily Plagiorchioidea. The four stages usually observed during vitellogenesis are described: stage I, cytoplasm of the vitellocytes mainly filled with ribosomes and few mitochondria; stage II, beginning of the synthetic activity; stage III, active synthesis of the shell globule clusters; stage IV, vitellocytes are filled with shell globule clusters and contain several lipid droplets, and glycogen granules are grouped around clusters and droplets. Vitellogenesis in P. elegans is compared with that of other Digenea. The differences among P. elegans and previously studied digeneans include, but are not limited to the occurrence of dense coiled endoplasmic reticulum saccules and the concentration of glycogen in the mesenchyme, which may be considered as a fifth stage of maturation of the vitelline glands. This peculiarity was not observed in all trematodes, which clearly indicates differences in the vitellogenesis in various digenean lineages at different stages of maturation of their vitelline cells.     

A new lasiosynid beetle from the Middle Jurassic of China with remarks on the systematic position of Lasiosynidae

A new beetle species, Lasiosyne laxa n. sp., is described from the Jurassic Daohugou deposits in Inner Mongolia, China. Its morphological significance and systematic position within the genus Lasiosyne Kirejtshuk et al., 2010a, Kirejtshuk et al., 2010b and the family Lasiosynidae are discussed. The research history of Lasiosynidae is summarized for the first time. The affiliation of Lasiosynidae to the superfamily Byrrhoidea is discussed in detail.     

Revision of the superfamily Acrotheloidea (Brachiopoda,class Linguliformea,order Lingulida) from the Lower and Middle Cambrian of the Siberian Platform

This paper continues our revision of Yu.L. Pelman’s collection of the superfamily Acrotheloidea (phosphatic brachiopods) and of our own material from the Early–Middle Cambrian of the Siberian Platform. The following representatives of the superfamily Acrotheloidea (order Lingulida, class Linguliformea) are restudied and revised based on new techniques: the genus Botsfordia (family Botsfordiidae Schindewolf, 1955) and the genera Acrothele, Eothele, and Orbithele (family Acrothelidae), which are widespread on the Siberian Platform. Only one out of the three Acrothele species described by Pelman is recognized as a valid species, and one new species of this genus that comprises some part of the brachiopods that Pelman figured and placed in another taxon is described. All these species are described using data on shell microsculpture and microstructure. In addition, the genera Eothele and Orbithele are described for the first time from the Siberian Platform.