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Superfamily
Kinds of Superfamily Terms modified by Superfamily Selected AbstractsStructure and Photoreaction of Photoactive Yellow Protein, a Structural Prototype of the PAS Domain Superfamily,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2007Yasushi Imamoto Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The ,/, fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p -coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed. [source] Cinnamic Acid Esters as Potent Inhibitors of Fungal 17,-Hydroxysteroid Dehydrogenase , A Model Enzyme of the Short-Chain Dehydrogenase/Reductase SuperfamilyCHEMINFORM, Issue 46 2004Stanislav Gobec Abstract For Abstract see ChemInform Abstract in Full Text. [source] New ways to break an old bond: the bacterial carbon,phosphorus hydrolases and their role in biogeochemical phosphorus cyclingENVIRONMENTAL MICROBIOLOGY, Issue 10 2007John P. Quinn Summary Phosphonates are organophosphorus molecules that contain the highly stable C,P bond, rather than the more common, and more labile, C,O,P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C,P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C,P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C,P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling. [source] Circuitry of nuclear factor ,B signalingIMMUNOLOGICAL REVIEWS, Issue 1 2006Alexander Hoffmann Summary:, Over the past few years, the transcription factor nuclear factor (NF)-,B and the proteins that regulate it have emerged as a signaling system of pre-eminent importance in human physiology and in an increasing number of pathologies. While NF-,B is present in all differentiated cell types, its discovery and early characterization were rooted in understanding B-cell biology. Significant research efforts over two decades have yielded a large body of literature devoted to understanding NF-,B's functioning in the immune system. NF-,B has been found to play roles in many different compartments of the immune system during differentiation of immune cells and development of lymphoid organs and during immune activation. NF-,B is the nuclear effector of signaling pathways emanating from many receptors, including those of the inflammatory tumor necrosis factor and Toll-like receptor superfamilies. With this review, we hope to provide historical context and summarize the diverse physiological functions of NF-,B in the immune system before focusing on recent advances in elucidating the molecular mechanisms that mediate cell type-specific and stimulus-specific functions of this pleiotropic signaling system. Understanding the genetic regulatory circuitry of NF-,B functionalities involves system-wide measurements, biophysical studies, and computational modeling. [source] The genomic context of natural killer receptor extended gene familiesIMMUNOLOGICAL REVIEWS, Issue 1 2001John Trowsdale Summary: The two sets of inhibitory and activating natural killer (NK) receptor genes belong either to the Ig or to the C-type lectin superfamilies. Both are extensive and diverse, comprising genes of varying degrees of relatedness, indicative of a process of iterative duplication. We have constructed gene maps to help understand how and when NK receptor genes developed and the nature of their polymorphism. A cluster of over 15 C-type lectin genes, the natural killer complex is located on human chromosome 12p13.1, syntenic with a region in mouse that borders multiple Ly49 loci. The equivalent locus in man is occupied by a single pseudogene, LY49L. The immunoglobulin superfamily of loci, the leukocyte receptor complex (LRC), on chromosome 19q13.4, contains many polymorphic killer cell immunoglobulin-like receptor (KIR) genes as well as multiple related sequences. These include immunoglobulin-like transcript (ILT) (or leukocyte immunoglobulin-like receptor genes), leukocyte-associated inhibitory receptor genes (LAIR), NKp46, Fc,R and the platelet glycoprotein receptor VI locus, which encodes a collagen-binding molecule. KIRs are expressed mostly on NK cells and some T cells. The other LRC loci are more widely expressed. Further centromeric of the LRC are sets of additional loci with weak sequence similarity to the KIRs, including the extensive CD66(CEA) and Siglec families. The LRC-syntenic region in mice contains no orthologues of KIRs. Some of the KIR genes are highly polymorphic in terms of sequence as well as for presence/absence of genes on different haplotypes. Some anchor loci, such as KIR2DL4, are present on most haplotypes. A few ILT loci, such as ILT5 and ILT8, are polymorphic, but only ILT6 exhibits presence/absence variation. This knowledge of the genomic organisation of the extensive NK superfamilies underpins efforts to understand the functions of the encoded NK receptor molecules. It leads to the conclusion that the functional homology of human KIR and mouse Ly49 genes arose by convergent evolution. NK receptor immunogenetics has interesting parallels with the major histocompatibility complex (MHC) in which some of the polymorphic genes are ligands for NK molecules. There are hints of an ancient genetic relationship between NK receptor genes and MHC-paralogous regions on chromosomes 1, 9 and 19. The picture that emerges from both complexes is of eternal evolutionary restlessness, presumably in response to resistance to disease. This work was funded by the Wellcome Trust and the MRC [source] Molecular phylogeny of Calyptratae (Diptera: Brachycera): the evolution of 18S and 16S ribosomal rDNAs in higher dipterans and their use in phylogenetic inferenceINSECT MOLECULAR BIOLOGY, Issue 5 2001X. Nirmala Abstract Sequences for nearly complete 18S rRNA and partial 16S rRNA genes were determined for sixteen species representing twelve calyptrate families. Two unique insertions are present in expansion regions of the 18S rDNA in nycteribiids. Alignments containing other dipteran rRNA genes provided good resolution at higher taxonomic level: monophyly of Calyptratae is well supported. While both 16S and 18S rDNA matrices produce unstable topologies within Calyptratae when analysed separately, their combination results in a tree with several robust and well supported nodes. Of three superfamilies recognized in recent classifications, the Hippoboscoidea is well supported by 16S rDNA and by combined matrices. The representatives of Muscoidea, Musca sp. and Antipoda sp., display a tendency to cluster within Oestroidea. The comparison of secondary structures of two variable regions indicates that Sarcophagidae are related to Calliphoridae rather than to Tachinidae. [source] Domain,ligand mapping for enzymesJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2010Matthew Bashton Abstract In this paper we provide an overview of our current knowledge of the mapping between small molecule ligands and protein domains. We give an overview of the present data resources available on the Web, which provide information about protein,ligand interactions, as well as discussing our own PROCOGNATE database. We present an update of ligand binding in large protein superfamilies and identify those ligands most frequently utilized by nature. Finally we discuss potential uses for this type of data. Copyright © 2009 John Wiley & Sons, Ltd. [source] Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn-superoxide dismutaseJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2008Fred J. Stevens Abstract The ,immunoglobulin-like' fold is one of most common structural motifs observed in proteins. This topology is found in more than 80 superfamilies of proteins, including Cu,Zn-superoxide dismutase (SOD) and cupredoxin. Evolutionary relationships have not been identified, but may exist. The challenge remains, therefore, of resolving the issue of whether the diverse distribution of the fold is accounted for by divergent evolution of function or convergent evolution of structure following multiple independent origins of function. Since the early studies that revealed conformational similarity of immunoglobulins and other proteins, the number of primary structures available for comparison has dramatically increased and new computational approaches for analysis of sequences have been developed. It now appears that a hypothesis of a common evolutionary origin for cupredoxins, Cu,Zn-SOD, and immunoglobulins may be credible. The distinction between protein homology and protein analogy is fundamental. The immunoglobulin-like fold may represent a robust system within which to examine again the issue of protein homology versus analogy. Copyright © 2007 John Wiley & Sons, Ltd. [source] Three-dimensional reconstruction of the odontophoral cartilages of Caenogastropoda (Mollusca: Gastropoda) using micro-CT: Morphology and phylogenetic significanceJOURNAL OF MORPHOLOGY, Issue 5 2009Rosemary E. Golding Abstract Odontophoral cartilages are located in the molluscan buccal mass and support the movement of the radula during feeding. The structural diversity of odontophoral cartilages is currently known only from limited taxa, but this information is important for interpreting phylogeny and for understanding the biomechanical operation of the buccal mass. Caenogastropods exhibit a wide variety of feeding strategies, but there is little comparative information on cartilage morphology within this group. The morphology of caenogastropod odontophoral cartilages is currently known only from dissection and histology, although preliminary results suggest that they may be structurally diverse. A comparative morphological survey of 18 caenogastropods and three noncaenogastropods has been conducted, sampling most major caenogastropod superfamilies. Three-dimensional models of the odontophoral cartilages were generated using X-ray microscopy (micro-CT) and reconstruction by image segmentation. Considerable morphological diversity of the odontophoral cartilages was found within Caenogastropoda, including the presence of thin cartilaginous appendages, asymmetrically overlapping cartilages, and reflexed cartilage margins. Many basal caenogastropod taxa possess previously unidentified cartilaginous support structures below the radula (subradular cartilages), which may be homologous to the dorsal cartilages of other gastropods. As subradular cartilages were absent in carnivorous caenogastropods, adaptation to trophic specialization is likely. However, incongruence with specific feeding strategies or body size suggests that the morphology of odontophoral cartilages is constrained by phylogeny, representing a new source of morphological characters to improve the phylogenetic resolution of this group. J. Morphol. 2009. © 2008 Wiley-Liss, Inc. [source] Evolution of the spermatozoon in muroid rodentsJOURNAL OF MORPHOLOGY, Issue 3 2005William G. Breed Abstract In the rodent superfamily Muroidea, a model for the evolution of sperm form has been proposed in which it is suggested that a hook-shaped sperm head and long tail evolved from a more simple, nonhooked head and short tail in several different subfamilies. To test this model the shape of the sperm head, with particular emphasis on its apical region, and length of sperm tail were matched to a recent phylogeny based on the nucleotide sequence of several protein-coding nuclear genes from 3 families and 10 subfamilies of muroid rodents. Data from the two other myomorph superfamilies, the Dipodoidea and kangaroo rats in the Geomyoidea, were used for an outgroup comparison. In most species in all 10 muroid subfamilies, apart from in the Murinae, the sperm head has a long rostral hook largely composed of acrosomal material, although its length and cross-sectional shape vary across the various subfamilies. Nevertheless, in a few species of various lineages a very different sperm morphology occurs in which an apical hook is lacking. In the outgroups the three species of dipodid rodents have a sperm head that lacks a hook, whereas in the heteromyids an acrosome-containing apical hook is present. It is concluded that, as the hook-shaped sperm head and long sperm tail occur across the muroid subfamilies, as well as in the heteromyid rodents, it is likely to be the ancestral condition within each of the subfamilies with the various forms of nonhooked sperm heads, that are sometimes associated with short tails, being highly derived states. These findings thus argue against a repeated evolution in various muroid lineages of a complex, hook-shaped sperm head and long sperm tail from a more simple, nonhooked sperm head and short tail. An alternative proposal for the evolution of sperm form within the Muroidea is presented in the light of these data. J. Morphol. © 2005 Wiley- Liss, Inc. [source] Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classificationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2008L. M. Tsang Abstract The infraorder Thalassinidea is a group of cryptic marine burrowing decapods of which the higher taxonomy is often contentious. The present analysis attempts to reconstruct phylogenetic relationship among 12 of the 13 currently recognized families using partial nuclear 18S, 28S rDNA and mitochondrial 16S rDNA sequences. The infraorder is divided into two distinct clades, with the first clade consisting of Thalassinidae, Laomediidae, Axianassidae and Upogebiidae, and the second clade including Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae and Callianideidae. Within the first clade, the Upogebiidae is the basal family. The Axianassidae shows low affinity to other laomediid genera indicating that it is a valid family. The interfamilial relationships are less well resolved in the second clade. The Axiidae is paraphyletic with respect to Calocarididae and Eiconaxiidae. Thus, the status of these two latter families is not supported if the currently defined Axiidae is maintained. All three families appear to be basal in the thalassinidean clade. The Micheleidae is closely related to the Callianideidae and they form a sister group to the Strahlaxiidae. The monophyletic Callianassidae aligns with the Micheleidae + Callianideidae + Strahlaxiidae clade. The relationship among the Axiidae + Calocarididae + Eiconaxiidae clade, Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae clade and the Ctenochelidae cannot be resolved which might be due to a rapid radiation of the three lineages. Our results do not support the generally used classification scheme of Thalassinidea and suggest that the infraorder might be divided into two superfamilies instead of three as suggested based on larval morphology, second pereiopod morphology in adults and gastric mill structure. The two superfamilies are Thalassinoidea (i.e. Thalassinidae, Laomediidae, Upogebiidae and Axianassidae) and Callianassoidea (i.e. Axioidea + Callianassoidea, as defined in Martin and Davis (2001) but excluding Laomediidae and Upogebiidae). It also appears that gill-cleaning adaptations are important in thalassinidean evolution while the presence of linea thalassinica is a result of parallel evolution. Résumé L'infraordre des Thalassinidea est un groupe de décapodes marins fouisseurs cryptiques dont la taxonomie au niveau supérieur est souvent controversée. Cette analyse tente de reconstruire les relations phylogénétiques entre 12 familles sur les 13 actuellement reconnues en utilisant les séquences partielles de rDNA nucléaire 18S, 28S et de rDNA mitochondrial 16S. L'infraordre est divisé en deux clades distincts, le premier comprenant les Thalassinidae, Laomediidae, Axianassidae et Upogebiidae, et le deuxième comprenant les Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae et Callianideidae. Dans le premier clade, les Upogebiidae est la famille basale. Les Axianassidae montre peu d'affinité avec les autres genres de laomedidés, ce qui indique que la famille est valide. Les relations interfamiliales sont moins bien résolues dans le second clade. La famille des Axiidae est paraphylétique par rapport aux Calocarididae et Eiconaxiidae. Ainsi le statut de ces deux dernières familles n'est pas supporté si la famille des Axiidae est maintenue dans sa définition actuelle. Toutes les trois familles apparaissent basales dans le clade thalassinidéen. La famille des Micheleidae est très proche des Callianideidae et elles forment un groupe frère des Strahlaxiidae. La famille monophylétique des Callianassidae s'aligne avec le clade Micheleidae + Callianideidae + Strahlaxiidae. La relation entre le clade Axiidae + Calocarididae + Eiconaxiidae, le clade des Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae et la famille des Ctenochelidae ne peut être résolue, ce qui pourrait être dûà une radiation rapide des trois lignées Nos résultats ne supportent pas le schéma de classification généralement utilisé pour les Thalassinidea et suggèrent que l'infraordre pourrait être divisé en deux superfamilles au lieu de trois comme suggéré sur la base de la morphologie larvaire, de la morphologie du deuxième péréiopode de l'adulte et de la structure du moulin gastrique. Les deux superfamilles sont: les Thalassinoidea (c'est-à-dire Thalassinidae, Laomediidae, Upogebiidae et Axianassidae) et Callianassoidea (c'est-à-dire Axioidea + Callianassoidea, comme définis dans Martin et Davis 2001 mais excluant les Laomediidae et les Upogebiidae). Il apparaît aussi que les adaptations pour le nettoyage des branchies sont importantes dans l'évolution thalassinidéenne alors que la présence de la linea thalassinica est le résultat d'une évolution parallèle. [source] Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classificationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2006C. D. Schubart Abstract Grapsoid and ocypodoid crabs receive a lot of attention in the literature due to their predominance and important role as primary and secondary consumers in intertidal as well as supratidal marine habitats. They are especially species-rich in the tropics, where they have been found to repeatedly invade terrestrial and freshwater habitats. However, the systematics of the crabs belonging to these two superfamilies is still not settled, despite recent steps clarifying phylogenetic relationships and introducing new taxa. In this study, a molecular phylogeny of grapsoid crabs primarily based on East African representatives is constructed based on DNA sequences of the mitochondrial small and large ribosomal subunits (12S and 16S rRNA), thus complementing previous molecular taxonomic studies that had been carried out with the American and East Asian fauna. In addition, selected representatives of all ocypodoid families and subfamilies were included. The monophyly of Grapsidae, Ocypodidae (sensu stuctu), Sesarmidae and Varunidae is well confirmed, if the genera Cyclograpsus, Helice are considered Varunidae and Euchirograpsus a Plagusiidae, as previously suggested. The monophyly of the family Gecarcinidae cannot be supported with our data. The family Plagusiidae in its present composition is polyphyletic. Special attention was given to the large family Sesarmidae, which has many endemic genera in the Indo-West Pacific. According to this study, two of the most speciose genera, Chiromantes and Parasesarma, are not monophyletic and need to be redefined. On the higher taxonomic level, it becomes evident that both superfamilies, Grapsoidea and Ocypodoidea, are not monophyletic in their current composition, as exemplified by a proposed sister group relationship of Varunidae and Macrophthalmidae. These results confirm those from previous molecular studies and we therefore propose to refrain from the traditional use of the Grapsoidea and Ocypodoidea as monophyletic superfamilies and treat the constituent families separately. Riassunto I granchi appartenenti alle superfamiglie Grapsoidea e Ocypodoidea da sempre sono oggetto di notevole interesse scientifico a causa del loro importante ruolo ecologico negli ambienti intertidali o sopratidali. Le due superfamiglie sono particolarmente rappresentate, in termini di numero di specie e d'abbondanza relativa, nelle zone tropicali e subtropicali, dove hanno invaso ripetutamente anche ambienti dulcacquicoli e terrestri. La sistematica delle specie appartenenti a queste due superfamiglie è ancora lontana dall'essere completamente risolta, nonostante studi molecolari recenti abbiano chiarito specifiche relazioni filogenetiche e definito nuovi taxa. Questo studio ha ricostruito la filogenesi di alcune specie di Grapsoidea dell'Africa Orientale sequenziando una porzione delle due subunità ribosomali del DNA mitocondriale (12S e 16S rRNA), confermando e completando precedenti studi molecolari condotti su specie americane e asiatiche. In questo studio sono stati inclusi anche rappresentanti di tutte le famiglie e sottofamiglie di ocipodidi. I nostri risultati confermano la monofilia della famiglia Grapsidae, Ocypodidae (sensu stuctu) Sesarmidae e Varunidae a condizione che, secondo quanto recentemente suggerito, i generi Cyclograpsus e Helice siano rimossi dalla famiglia Sesarmidae ed attribuiti ai Varunidae, ed Euchirograpsus dalla famiglia Varunidae ai Plagusiidae. Invece, i nostri dati supportano solo debolmente o non supportano per niente la monofilia della famiglia Gecarcinidae. La famiglia Plagusiidae è probabilmente polifiletica. Questo studio pone inoltre particolare attenzione alle relazioni interne alla famiglia Sesarmidae che include molti generi endemici nell'area Indo-Pacifica occidentale. Sulla base dei nostri dati, i generi Chiromantes, Parasesarma e Perisesarma sono polifiletici e necessitano di essere ridefiniti. Infine, i risultati di questo studio mostrano chiaramente che la superfamiglia Grapsoidea e Ocypodidea non sono monofiletiche così come attualmente definite, come evidenziato dalla relazione di sister group tra Varunidae e Macropthalmidae. Questo conferma i risultati di precedenti studi molecolari e pertanto proponiamo di non attenersi al tradizionale uso delle superfamiglie Grapsoidea ed Ocypodoidea. [source] Tuberculate micro-ornament on the juvenile shell of Middle Jurassic ammonoidsLETHAIA, Issue 1 2001Anton M. Sprey In two genera of Callovian Ammonitina of distinct superfamilies, the juvenile shell displays a tuberculate micro-ornament in addition to growth lines. In contrast to the circular micro-tubercles of the ammonitella shell, post-embryonic tubercles are oval to longish in outline. They are arranged in rows running parallel to the growth lines in Kosmoceras (Spinikosmoceras) and cross the growth lines in Binatisphinctes. [source] House cleaning, a part of good housekeepingMOLECULAR MICROBIOLOGY, Issue 1 2006Michael Y. Galperin Summary Cellular metabolism constantly generates by-products that are wasteful or even harmful. Such compounds are excreted from the cell or are removed through hydrolysis to normal cellular metabolites by various ,house-cleaning' enzymes. Some of the most important contaminants are non-canonical nucleoside triphosphates (NTPs) whose incorporation into the nascent DNA leads to increased mutagenesis and DNA damage. Enzymes intercepting abnormal NTPs from incorporation by DNA polymerases work in parallel with DNA repair enzymes that remove lesions produced by modified nucleotides. House-cleaning NTP pyrophosphatases targeting non-canonical NTPs belong to at least four structural superfamilies: MutT-related (Nudix) hydrolases, dUTPase, ITPase (Maf/HAM1) and all-, NTP pyrophosphatases (MazG). These enzymes have high affinity (Km's in the micromolar range) for their natural substrates (8-oxo-dGTP, dUTP, dITP, 2-oxo-dATP), which allows them to select these substrates from a mixture containing a ,1000-fold excess of canonical NTPs. To date, many house-cleaning NTPases have been identified only on the basis of their side activity towards canonical NTPs and NDP derivatives. Integration of growing structural and biochemical data on these superfamilies suggests that their new family members cleanse the nucleotide pool of the products of oxidative damage and inappropriate methylation. House-cleaning enzymes, such as 6-phosphogluconolactonase, are also part of normal intermediary metabolism. Genomic data suggest that house-cleaning systems are more abundant than previously thought and include numerous analogous enzymes with overlapping functions. We discuss the structural diversity of these enzymes, their phylogenetic distribution, substrate specificity and the problem of identifying their true substrates. [source] The putative l -lactate dehydrogenase from Methanococcus jannaschii is an NADPH-dependent l -malate dehydrogenaseMOLECULAR MICROBIOLOGY, Issue 6 2000Dominique Madern The enyme encoded by Methanococcus jannaschii open reading frame (ORF) 0490 was purified and characterized. It was shown to be an NADPH-dependent [lactate dehydrogenase (LDH)-like]l -malate dehydrogenase (MalDH) and not an l -lactate dehydrogenase, as had been suggested previously on the basis of amino acid sequence similarity. The results show the importance of biochemical data in the assignment of ORF function in genomic sequences and have implications for the phylogenetic distribution of members of the MalDH/LDH enzyme superfamilies within the prokaryotic kingdom. [source] The adipokinetic hormones of Heteroptera: a comparative studyPHYSIOLOGICAL ENTOMOLOGY, Issue 2 2010DALIBOR KODRÍK The adipokinetic hormones (AKHs) from 15 species of heteropteran Hemiptera (encompassing eight families, six superfamilies and three infraorders) have been isolated and structurally identified using liquid chromatography coupled with mass spectrometry. None of the structures are novel and all are octapeptides. These peptide sequence data are used, together with the previously available AKH sequence data on Heteroptera, to create a larger dataset for comparative analyses. This results, in total, in AKH sequences from 30 species (spanning 13 families), which are used in a matrix confronted with the current hypotheses on the phylogeny of Heteroptera. The expanded dataset shows that all heteropterans have octapeptide AKHs; three species have two AKHs, whereas the overwhelming majority have only one AKH. From a total of 11 different AKH peptides known from Heteroptera to date, three AKHs occur frequently: Panbo-red pigment-concentrating hormone (RPCH) (×10), Schgr-AKH-II (×6) and Anaim-AKH (×4). The heteropteran database also suggests that particular AKH variants are family-specific. The AKHs of Heteroptera: Pentatomomorpha (all terrestrial) are not present in Nepomorpha (aquatic) and Gerromorpha: Gerridae (semiaquatic); AKHs with a Val in position 2 are absent in the Pentatomomorpha (only AKHs with Leu2 are present), whereas Val2 predominates in the nonterrestrial species. An unexpected diversity of AKH sequences is found in Nepomorpha, Nepoidea, Nepidae and Nepinae, whereas Panbo-RPCH (which has been identified in all infraorders of decapod crustaceans) is present in all analysed species of Pentatomidae and also in the only species of Tessaratomidae investigated. The molecular evolution of Heteroptera with respect to other insect groups and to crustaceans is discussed [source] Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: A special subgroup of the type III extradiol dioxygenasesPROTEIN SCIENCE, Issue 4 2006Xiaowu Li Abstract 3-Hydroxyanthranilic acid 3,4-dioxygenase (3HAO) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA) receptors and the precursor of NAD+ biosynthesis. The crystal structure of 3HAO from S. cerevisiae at 2.4 Å resolution shows it to be a member of the functionally diverse cupin superfamily. The structure represents the first eukaryotic 3HAO to be resolved. The enzyme forms homodimers, with two nickel binding sites per molecule. One of the bound nickel atoms occupies the proposed ferrous-coordinated active site, which is located in a conserved double-strand ,-helix domain. Examination of the structure reveals the participation of a series of residues in catalysis different from other extradiol dioxygenases. Together with two iron-binding residues (His49 and Glu55), Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101, Gln59, and the substrate-binding hydrophobic pocket are crucial for substrate specificity. Structure comparison with 3HAO from Ralstonia metallidurans reveals similarities at the active site and suggests the same catalytic mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence comparison, we suggest that bicupin of human 3HAO is the first example of evolution from a monocupin dimer to bicupin monomer in the diverse cupin superfamilies. Based on the model of the substrate HAA at the active site of Y3HAO, we propose a mechanism of catalysis for 3HAO. [source] Assessing strategies for improved superfamily recognitionPROTEIN SCIENCE, Issue 7 2005Ian Sillitoe Abstract There are more than 200 completed genomes and over 1 million nonredundant sequences in public repositories. Although the structural data are more sparse (,13,000 nonredundant structures solved to date), several powerful sequence-based methodologies now allow these structures to be mapped onto related regions in a significant proportion of genome sequences. We review a number of publicly available strategies for providing structural annotations for genome sequences, and we describe the protocol adopted to provide CATH structural annotations for completed genomes. In particular, we assess the performance of several sequence-based protocols employing Hidden Markov model (HMM) technologies for superfamily recognition, including a new approach (SAMOSA [sequence augmented models of structure alignments]) that exploits multiple structural alignments from the CATH domain structure database when building the models. Using a data set of remote homologs detected by structure comparison and manually validated in CATH, a single-seed HMM library was able to recognize 76% of the data set. Including the SAMOSA models in the HMM library showed little gain in homolog recognition, although a slight improvement in alignment quality was observed for very remote homologs. However, using an expanded 1D-HMM library, CATH-ISL increased the coverage to 86%. The single-seed HMM library has been used to annotate the protein sequences of 120 genomes from all three major kingdoms, allowing up to 70% of the genes or partial genes to be assigned to CATH superfamilies. It has also been used to recruit sequences from Swiss-Prot and TrEMBL into CATH domain superfamilies, expanding the CATH database eightfold. [source] Finding evolutionary relations beyond superfamilies: Fold-based superfamiliesPROTEIN SCIENCE, Issue 10 2003Keiko Matsuda Abstract Superfamily classifications are based variably on similarity of sequences, global folds, local structures, or functions. We have examined the possibility of defining superfamilies purely from the viewpoint of the global fold/function relationship. For this purpose, we first classified protein domains according to the ,-sheet topology. We then introduced the concept of kinship relations among the classified ,-sheet topology by assuming that the major elementary event leading to creation of a new ,-sheet topology is either an addition or deletion of one ,-strand at the edge of an existing ,-sheet during the molecular evolution. Based on this kinship relation, a network of protein domains was constructed so that the distance between a pair of domains represents the number of evolutionary events that lead one from the other domain. We then mapped on it all known domains with a specific core chemical function (here taken, as an example, that involving ATP or its analogs). Careful analyses revealed that the domains are found distributed on the network as >20 mutually disjointed clusters. The proteins in each cluster are defined to form a fold-based superfamily. The results indicate that >20 ATP-binding protein superfamilies have been invented independently in the process of molecular evolution, and the conservative evolutionary diffusion of global folds and functions is the origin of the relationship between them. [source] Three monophyletic superfamilies account for the majority of the known glycosyltransferasesPROTEIN SCIENCE, Issue 7 2003Jing Liu Abstract 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. [source] The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicumPROTEIN SCIENCE, Issue 6 2002Dinesh Christendat Abstract As part of our structural proteomics initiative, we have determined the crystal structure of MTH1491, a previously uncharacterized hypothetical protein from Methanobacterium thermoautotrophicum. MTH1491 is one of numerous structural genomics targets selected in a genome-wide survey of uncharacterized proteins. It belongs to a family of proteins whose biological function is not known. The crystal structure of MTH1491, the first structure for this family of proteins, consists of an overall five-stranded parallel ,-sheet with strand order 51234 and flanking helices. The oligomeric form of this molecule is a trimer as seen from both crystal contacts and gel filtration studies. Analysis revealed that the structure of MTH1491 is similar to that of dehydrogenases, amidohydrolases, and oxidoreductases. Using a combination of sequence and structural analyses, we showed that MTH1491 does not belong to either the dehydrogenase or the amidohydrolase superfamilies of proteins. [source] Multiple diverse ligands binding at a single protein site: A matter of pre-existing populationsPROTEIN SCIENCE, Issue 2 2002Buyong Ma Abstract Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations. All proteins, specific and nonspecific, exist in ensembles of substates. If the library of ligands in solution is large enough, favorably matching ligands with altered shapes and sizes can be expected to bind, with a redistribution of the protein populations. Point mutations at spatially distant sites may exert large conformational rearrangements and hinge effects, consistent with mutations away from the binding site leading to population shifts and (cross-)drug resistance. A similar effect is observed in protein superfamilies, in which different sequences with similar topologies display similar large-scale dynamic motions. The hinges are frequently at analogous sites, yet with different substrate specificity. Similar topologies yield similar conformational isomers, although with different distributions of population times, owing to the change in the conditions, that is, the change in the sequences. In turn, different distributions relate to binding of different sizes and shapes. Hence, the binding site shape and size are defined by the ligand. They are not independent entities of fixed proportions and cannot be analyzed independently of the binding partner. Such a proposition derives from viewing proteins as dynamic distributions, presenting to the incoming ligands a range of binding site shapes. It illustrates how presumably specific binding molecules can bind multiple ligands. In terms of drug design, the ability of a single receptor to recognize many dissimilar ligands shows the need to consider more diverse molecules. It provides a rationale for higher affinity inhibitors that are not derived from substrates at their transition states and indicates flexible docking schemes. [source] CXC and CC chemokines induced in human renal epithelial cells by inflammatory cytokinesAPMIS, Issue 7 2009ELISKA THORBURN (NEE KRASNA) Human renal epithelial cells might play an important role during the allograft rejection by producing chemokines in response to proinflammatory cytokines such as tumor necrosis factor (TNF)-, and interleukin (IL)-1, produced by endothelial and epithelial cells early after transplantation. The production of chemokines allows inflammatory cells to be drawn into the kidney graft and therefore plays a critical role in the pathophysiologic processes that lead to the rejection of renal transplant. In this process, two chemokine superfamilies, the CC and the CXC chemokines, are the most important. The CC chemokines target mainly monocytes and T lymphocytes, while most of the CXC chemokines attract neutrophils. We showed in our study that in vitro, in unstimulated cells, basal mRNA expression of CXC chemokines (Gro,, Gro,, Gro,, ENA-78 and GCP-2, IL-8) that attract neutrophils was detectable and expression of these genes and chemokine release were increased in TNF-,- and IL-1,-induced renal epithelial cells. Most of the CC chemokines [monocyte chemotactic protein-1 (MCP-1), macrophage Inflammatory protein 1 beta (MIP-1,), regulated upon activation, normal T cell expressed and secreted (RANTES) and macrophage inflammatory protein (MIP-3,)] showed detectable mRNA expression only after stimulation with proinflammatory cytokines and not in control cells. TNF-, seems to induce preferably the expression of RANTES, MCP-1, interferon-inducible protein (IP-10) and Interferon-Inducible T-cell Alpha Chemoattractant (I-TAC), while IL-1, induces mainly IL-8 and epithelial neutrophil-activating peptide 78 (ENA-78). [source] Simultaneous analysis of basal Hymenoptera (Insecta): introducing robust-choice sensitivity analysisBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2003SUSANNE SCHULMEISTER Molecular characters are analysed on their own and in combination with morphological data to examine the phylogenetic relationships of the basal lineages of Hymenoptera (,Symphyta'). This study covers 47 sawfly genera and nine apocritan families and includes molecular sequences from five genes , 12S, 16S, 18S and 28S ribosomal genes and cytochrome oxidase 1 , as well as 343 morphological characters. A robust-choice sensitivity analysis is performed with the data. First, the simultaneous analysis is repeated three times, each time employing a different step matrix for weighting the transformations of the molecular characters. Then, the results of all three simultaneous analyses are summarized in a strict consensus in order to avoid basing the conclusions on a narrow set of assumptions. This methodology is discussed in the paper. The relationships among superfamilies largely confirm previous hypotheses, being (Xyeloidea (Tenthredinoidea s.l. (Pamphilioidea (Cephoidea (Siricoidea (Xiphydrioidea (Orussoidea Apocrita))))))), where Siricoidea is understood as Siricidae+Anaxyelidae. However, the relationships within Tenthredinoidea s.s. proposed here are novel: ({Argidae Pergidae}[Athalia{(Diprionidae Cimbicidae) Tenthredinidae minus Athalia}]). © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79, 245,275. [source] Current Knowledge of Mesozoic Coleoptera from Daohugou and Liaoning (Northeast China)ACTA GEOLOGICA SINICA (ENGLISH EDITION), Issue 4 2010Alexander G. KIREJTSHUK Abstract: The present paper is devoted to an overview on fossil Coleoptera studied from Inner Mongolia, Daohugou (Middle Jurassic, Jiulongshan Formation) and Liaoning (Upper Jurassic-Lower Cretaceous, Yixian Formation) deposited in Chinese collections. As a result, species of the tribe Sperchopsini and Hydrophilini from Hydrophilidae, families and subfamilies Silphidae, Syndesinae from Lucanidae, Pleocomidae, Trogidae, Trogissitidae, Pyrochroidae, Diaperinae from Tenebrionidae, and Cerambycidae were first registered in the Mesozoic and some families were defined as new. It was shown that many superfamilies represented in the Recent Fauna were formed within the Middle Jurassic and Lower Cretaceous. The materials examined confirm the hypothesis that Cucujiformian beetles are a younger group than other infraordera of Polyphaga (Staphyliniformia and Elateriformia) and, therefore, they appeared in the fossil record only in the late Mesozoic. It was shown and confirmed that most superfamilies appeared in the fossil records before Cucujoidea. The synonymy of Notocupes Ponomarenko, 1964; Sinocupes Lin, 1976, syn. nov.; Amblomma Tan, Ren et Liu 2005, syn. nov.; Euryomma Tan, Ren et Shih, 2006, syn. nov., non Stein, 1899 and Ovatocupes Tan et Ren, 2006, syn. nov.; synonymy of Tetraphalerus Waterhouse, 1901 and Odontomma Tan, Ren et Ge 2006, syn. nov.; and synonymy of Priacmopsis Ponomarenko, 1966 and Latocupes Tan et Ren, 2006, syn. nov. are proposed. Sinorhombocoleus papposus Tan et Ren, 2009 is transferred from the family Rhombocoleidae to Schizophoridae. Cervicatinius complanus Tan, Ren et Shih, 2007 and Forticatinius elegans Tan, Ren et Shih, 2007 are transferred from the family Catiniidae (suborder Archostemata) to superfamily Cleroidea (suborder Polyphaga: first among the family Peltidae and second as a closely related group to the latter family). The family Parandrexidae is transferred from the superfamily Cucujoidea to Cleroidea. The ecological circumstances of the past ecosystems and hypotheses of historical development of the order Coleoptera are discussed. The age of faunas examined is considered. The list of the taxa described from Daohugou and Liaoning is compiled. [source] 4252: An introduction to autoinflammatory syndromesACTA OPHTHALMOLOGICA, Issue 2010B BODAGHI To define the spectrum and pathophysiology of autoinflammatory syndromes. This term has been proposed to describe a new group of diseases characterized by attacks of seemingly unprovoked inflammation in the absence of pathogens, without significant levels of autoantibodies and autoreactive T cells. Hereditary periodic fever syndrome, Crohn's disease, Blau syndrome, Chronic infantile neurologic cutaneous and articular syndrome and Muckle-Wells syndrome are examples of autoinflammatory conditions characterized by recurrent attacks of inflammation without any association with auto-antigens. The study of autoinflammatory diseases has progressed from genetics to definition of the functional defects. Although a direct association between defective innate immune responses to bacterial components and these diseases has not been established yet, this hypothesis remains highly plausible. Mutations in genes encoding the tumour necrosis factor (TNF) receptor and pyrin superfamilies of molecules may induce persistence of leukocytes that would ordinarily undergo apoptosis with further amplification of inflammatory stimuli. The use of biologics may control some of these conditions. [source] The Arabidopsis class VIII myosin ATM2 is involved in endocytosisCYTOSKELETON, Issue 6 2008Amirali Sattarzadeh Abstract Members of the class XI of the myosin superfamily comprising higher plant, actin-based molecular motors have been shown to be involved in peroxisome and Golgi vesicle trafficking comparable to yeast and animal class V myosins. The tasks of the second class of myosins of higher plants, class VIII, are unclear. In this study the class VIII myosin ATM2 from the model plant Arabidopsis thaliana was selected for the examination of cargo specificity in vivo. Fluorescent protein-fusion plasmid constructs with fragments of the ATM2 cDNA were generated and used for Agrobacterium tumefaciens -based transient transformation of Nicotiana benthamiana leaves. The resulting subcellular localization patterns were recorded by live imaging with confocal laser scanning microscopy (CLSM) in epidermal leaf cells. Expression of a nearly full-length construct displayed labeling of filaments and vesicles, a head + neck fragment led to decoration of filaments only. However, expression of fluorescent protein-tagged C-terminal tail domain constructs labeled vesicular structures of different appearance. Most importantly, coexpression of different RFP/YFP-ATM2 tail fusion proteins showed colocalization and, hence, binding to the same type of vesicular target. Further coexpression experiments of RFP/YFP-ATM2 tail fusion proteins with the endosomal marker FYVE and the endosomal tracer FM4-64 demonstrated colocalization with endosomes. Colocalization was also detected by expression of the CFP-tagged membrane receptor BRI1 as marker, which is constantly recycled via endosomes. Occasionally the ATM2 tail targeted to sites at the plasma membrane closely resembling the pattern obtained upon expression of the YFP-ATM1 C-terminal tail. ATM1 is known for its localization at the plasma membrane at sites of plasmodesmata. Cell Motil. Cytoskeleton 2008. © 2008 Wiley-Liss, Inc. [source] Pleiotropic function of FGF-4: Its role in development and stem cellsDEVELOPMENTAL DYNAMICS, Issue 2 2009Nobuyoshi Kosaka Abstract Fibroblast growth factors (FGFs) were initially recognized as fibroblast-specific growth factor, and it is now apparent that these growth factors regulate multiple biological functions. The diversity of FGFs function is paralleled by the emerging diversity of interactions between FGF ligands and their receptors. FGF-4 is a member of the FGF superfamily and is a mitogen exhibiting strong action on numerous different cell types. It plays a role in various stages of development and morphogenesis, as well as in a variety of biological processes. Recent studies reveal the molecular mechanisms of FGF-4 gene regulation in mammalian cells, which is involved in the developmental process. Furthermore, FGF-4 also acts on the regulation of proliferation and differentiation in embryonic stem cells and tissue stem cells. In this review, we focus on the diverse biological functions of FGF-4 in the developmental process and also discuss its putative roles in stem cell biology. Developmental Dynamics 238:265,276, 2009. © 2008 Wiley-Liss, Inc. [source] Cysteine-rich secretory proteins are not exclusively expressed in the male reproductive tractDEVELOPMENTAL DYNAMICS, Issue 11 2008Thulasimala Reddy The Cysteine-RIch Secretory Proteins (CRISPs) are abundantly produced in the male reproductive tract of mammals and within the venom of reptiles and have been shown to regulate ion channel activity. CRISPs, along with the Antigen-5 proteins and the Pathogenesis related-1 (Pr-1) proteins, form the CAP superfamily of proteins. Analyses of EST expression databases are increasingly suggesting that mammalian CRISPs are expressed more widely than in the reproductive tract. We, therefore, conducted a reverse transcription PCR expression profile and immunohistochemical analyses of 16 mouse tissues to define the sites of production of each of the four murine CRISPs. These data showed that each of the CRISPs have distinct and sometimes overlapping expression profiles, typically associated with the male and female reproductive tract, the secretory epithelia of exocrine glands, and immune tissues including the spleen and thymus. These investigations raise the potential for a role for CRISPs in general mammalian physiology. Developmental Dynamics 237:3313,3323, 2008. © 2008 Wiley-Liss, Inc. [source] Identification of candidate secreted factors involved in trigeminal placode inductionDEVELOPMENTAL DYNAMICS, Issue 10 2007Kathryn L. McCabe Abstract Cranial ectodermal placodes are critical for normal development of the peripheral nervous system of the head. However, many aspects of the molecular and tissue interactions involved in their induction have yet to be elucidated. The trigeminal placode is induced by an unidentified secreted factor(s) from the dorsal neural tube. To determine candidates that may be involved in this induction process, we have performed reverse transcriptase-polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization to screen for receptors expressed by uninduced presumptive trigeminal level ectoderm. We have found that receptors for fibroblast growth factors, insulin-like growth factors, platelet-derived growth factors, Sonic hedgehog, the transforming growth factor-beta superfamily, and Wnts all are expressed in patterns consistent with a role in trigeminal placode formation. This RT-PCR screen for candidate receptors expressed in presumptive trigeminal ectoderm is the first systematic screen to identify potential interactions underlying induction of the trigeminal placode and represents a critical step for understanding this complex process. Developmental Dynamics 236:2925,2935, 2007. © 2007 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||||||||||||||