High Degree Of Sequence Identity Research Articles

Two differentially active alternative promoters control the expression of the zebrafish orphan nuclear receptor gene Rev-erbα

The orphan nuclear receptor Rev-erbalpha (NR1D1) plays an important role in the regulation of the circadian pacemaker and its expression has been shown to be regulated with a robust circadian rhythm in zebrafish and mammals. In addition, in zebrafish its expression has been shown to be developmentally regulated. In order to analyze the mechanisms of the zfRev-erbalpha gene regulation, we have isolated its 5'-upstream region. We found that two promoters control the zfRev-erbalpha expression. The first one (ZfP1) is characterized by a very high degree of sequence identity with the mammalian P1 promoter and contains, as the mammalian P1, a functional Rev-erbalpha-binding site (RevDR2). Inhibition of zfRev-erbalpha activity in zebrafish embryos using antisense-morpholino knockdown results in an increase of zfRev-erbalpha gene expression suggesting that zfRev-erbalpha is repressing its own transcription in vivo. In addition, we show that ROR orphan receptors also regulate in vitro and in vivo zfRev-erbalpha gene expression through the same RevDR2 element. In contrast, the second promoter ZfP2 is strikingly different from the mammalian P2: its sequence is not conserved between zebrafish and mammals and is not regulated by the same transcription factors. Together, these data suggest that ZfP1 is orthologous to the mammalian P1 promoter, whereas zebrafish ZfP2 has no mammalian ortholog and does not function like ZfP1 to control Rev-erbalpha expression.

Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk

Antimicrobial resistance in Yersinia pestis is rare, yet constitutes a significant international public health and biodefense threat. In 1995, the first multidrug resistant (MDR) isolate of Y. pestis (strain IP275) was identified, and was shown to contain a self-transmissible plasmid (pIP1202) that conferred resistance to many of the antimicrobials recommended for plague treatment and prophylaxis. Comparative analysis of the DNA sequence of Y. pestis plasmid pIP1202 revealed a near identical IncA/C plasmid backbone that is shared by MDR plasmids isolated from Salmonella enterica serotype Newport SL254 and the fish pathogen Yersinia ruckeri YR71. The high degree of sequence identity and gene synteny between the plasmid backbones suggests recent acquisition of these plasmids from a common ancestor. In addition, the Y. pestis pIP1202-like plasmid backbone was detected in numerous MDR enterobacterial pathogens isolated from retail meat samples collected between 2002 and 2005 in the United States. Plasmid-positive strains were isolated from beef, chicken, turkey and pork, and were found in samples from the following states: California, Colorado, Connecticut, Georgia, Maryland, Minnesota, New Mexico, New York and Oregon. Our studies reveal that this common plasmid backbone is broadly disseminated among MDR zoonotic pathogens associated with agriculture. This reservoir of mobile resistance determinants has the potential to disseminate to Y. pestis and other human and zoonotic bacterial pathogens and therefore represents a significant public health concern.

Molecular cloning of three types of arginine vasotocin receptor in the newt, Cynops pyrrhogaster

Three types of cDNA encoding the arginine vasotocin (AVT) receptors from the newt, Cynops pyrrhogaster were cloned and the gene expression of each receptor analyzed in the organs and tissues of the newt. The deduced amino acid sequence of one type of AVT receptor, consisting of 418 amino acid residues, showed a high degree of sequence identity with the mammalian arginine vasopressin (AVP) V1a receptors (61–68%). The second type of cDNA, encoding an amino acid sequence consisting of 367 amino acid residues, exhibited a relatively high sequence identity with mammalian AVP V2 receptors (50–51%). The third cDNA, encoding a sequence of 415 amino acid residues, possessed high sequence identity with mammalian AVP V3/V1b receptors (59–63%). Phylogenetic analysis revealed that the first, second and third types of receptor were close to mammalian AVP V1a, V2 and V3/V1b receptors, respectively, and RT-PCR using gene specific primers for each type of receptor indicated that the first and second types of receptor mRNA were expressed in various organs and tissues, including the circulatory, osmoregulatory, and reproductive organs of both male and female newts. In contrast, mRNA expression of the third cDNA was mainly detected in the brain and pituitary, and its expression pattern was distinctly different from that of the other two. We suggest that the first, second and third types of newt AVT receptor obtained in the present study are counterparts of mammalian AVP V1a, V2 and V3/V1b receptors, respectively.

Structural Basis for Spinophilin−Neurabin Receptor Interaction

Neurabin and spinophilin are neuronal scaffolding proteins that play important roles in the regulation of synaptic transmission through their ability to target protein phosphatase 1 (PP1) to dendritic spines where PP1 dephosphorylates and inactivates glutamate receptors. However, thus far, it is still unknown how neurabin and spinophilin themselves are targeted to these membrane receptors. Spinophilin and neurabin contain a single PDZ domain, a common protein-protein interaction recognition motif, which are 86% identical in sequence. We report the structures of both the neurabin and spinophilin PDZ domains determined using biomolecular NMR spectroscopy. These proteins form the canonical PDZ domain fold. However, despite their high degree of sequence identity, there are distinct and significant structural differences between them, especially between the peptide binding pockets. Using two-dimensional 1H-15N HSQC NMR analysis, we demonstrate that C-terminal peptide ligands derived from glutamatergic AMPA and NMDA receptors and cytosolic proteins directly and differentially bind spinophilin and neurabin PDZ domains. This peptide binding data also allowed us to classify the neurabin and spinophilin PDZ domains as the first identified neuronal hybrid class V PDZ domains, which are capable of binding both class I and II peptides. Finally, the ability to bind to glutamate receptor subunits suggests that the PDZ domains of neurabin and spinophilin are important for targeting PP1 to C-terminal phosphorylation sites in AMPA and NMDA receptor subunits.

Characterization of a Plant-like Protochlorophyllide a Divinyl Reductase in Green Sulfur Bacteria

The green sulfur bacterium Chlorobium tepidum synthesizes three types of (bacterio)chlorophyll ((B)Chl): BChl a(P), Chl a(PD), and BChl c(F). During the synthesis of all three molecules, a C-8 vinyl substituent is reduced to an ethyl group, and in the case of BChl c(F), the C-8(2) carbon of this ethyl group is subsequently methylated once or twice by the radical S-adenosylmethionine enzyme BchQ. The C. tepidum genome contains homologs of two genes, bchJ (CT2014) and CT1063, that are highly homologous to genes, bchJ and AT5G18660, and that have been reported to encode C-8 vinyl reductases in Rhodobacter capsulatus and Arabidopsis thaliana, respectively. To determine which gene product actually encodes a C-8 vinyl reductase activity, the bchJ and CT1063 genes were insertionally inactivated in C. tepidum. All three Chls synthesized by the CT1063 mutant of C. tepidum have a C-8 vinyl group. Using NADPH but not NADH as reductant, recombinant BciA reduces the C-8 vinyl group of 3,8-divinyl-protochlorophyllide in vitro. These data demonstrate that CT1063, renamed bciA, encodes a C-8 divinyl reductase in C. tepidum. The bchJ mutant produces detectable amounts of Chl a(PD), BChl a(P), and BChl c(F), all of which have reduced C-8 substituents, but the mutant cells secrete large amounts of 3,8-divinyl-protochlorophyllide a into the growth medium and have a greatly reduced BChl c(F) content. The results suggest that BchJ may play an important role in substrate channeling and/or regulation of Chl biosynthesis but show that it is not a vinyl reductase. Because only some Chl-synthesizing organisms possess homologs of bciA, at least two types of C-8 vinyl reductases must occur.

Folding Mechanisms of Proteins with High Sequence Identity but Different Folds

The problem of how a protein folds from a linear chain of amino acids to the three-dimensional structure necessary for function is often investigated using proteins with a low degree of sequence identity that adopt different folds. The design of pairs of proteins with a high degree of sequence identity but different folds offers the opportunity for a complementary study; in two highly similar sequences, which residues are the most important in directing folding to a particular structure? Here we use molecular dynamics simulations to characterize the folding-unfolding pathways of a pair of proteins designed by Bryan and co-workers [Alexander, P. A., et al. (2005) Biochemistry 44, 14045-14054; He, Y. N., et al. (2005) Biochemistry 44, 14055-14061]. Despite being 59% identical, the two protein sequences fold to two different structures. The first sequence folds to the alpha+beta protein G structure and the second to the all-alpha-helical protein A structure. We show that the final protein structure is determined early along the folding pathway. In folding to the protein G structure, the single alpha-helix (alpha1) and the beta3-beta4 turn fold early. Formation of the hairpin turn essentially prevents folding to helical structure in this region of the protein. This early structure is then consolidated by formation of long-range hydrophobic interactions between alpha1 and the beta3-beta4 turn. The protein A sequence differs both in the residues that form the beta3-beta4 turn and also in many of the residues that form the early hydrophobic interactions in the protein G structure. Instead, in the protein A sequence, a more hierarchical mechanism is observed, with helices folding before many of the tertiary interactions are formed. We find that small, but critical, sequence differences determine the topology of the protein early along the folding pathway, which help to explain the process by which one fold can evolve into another.

GENETIC DIVERSITY IN SNAKE VENOM THREE-FINGER PROTEINS AND PHOSPHOLIPASE A2 ENZYMES

Based on genetic organization and high degree of sequence identity, three-finger protein genes and phospholipase A2 genes appear to represent two multigene families in snake genomes. Unlike intron insertions or deletions, the evolution of protein coding regions of these genes is accelerated by adaptive selection. Thus, the protein coding regions of the two multigene families are more diversified than their intron regions. Alternatively, genetic elements in regulating protein expression were mostly retained during the evolution of the two multigene families. These observations indicate that the multiplicity of the two multigene families expanded on their ancestral gene by gene duplication followed by divergence, and suggest a common route for the evolution of snake toxins.

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that is activated by a structurally diverse array of synthetic and natural chemicals, including toxic halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Analysis of the molecular events occurring in the AhR ligand binding and activation processes requires structural information on the AhR Per-Arnt-Sim (PAS) B-containing ligand binding domain, for which no experimentally determined structure has been reported. With the availability of extensive structural information on homologous PAS-containing proteins, a reliable model of the mouse AhR PAS B domain was developed by comparative modeling techniques. The PAS domain structures of the functionally related hypoxia-inducible factor 2alpha (HIF-2alpha) and AhR nuclear translocator (ARNT) proteins, which exhibit the highest degree of sequence identity and similarity with AhR, were chosen to develop a two-template model. To confirm the features of the modeled domain, the effects of point mutations in selected residue positions on both TCDD binding to the AhR and TCDD-dependent transformation and DNA binding were analyzed. Mutagenesis and functional analysis results are consistent with the proposed model and confirm that the cavity modeled in the interior of the domain is indeed involved in ligand binding. Moreover, the physicochemical characteristics of some residues and of their mutants, along with the effects of mutagenesis on TCDD and DNA binding, also suggest some key features that are required for ligand binding and activation of mAhR at a molecular level, thus providing a framework for further studies.

Candidate pheromone binding proteins of the silkmoth Bombyx mori

Pheromone reception is thought to be mediated by pheromone binding proteins (PBPs) in the aqueous lymph of the antennal sensilla. Recent studies have shown that the only known PBP of Bombyx mori (BmorPBP1) appears to be specifically tuned to bombykol but not to bombykal, raising the question of whether additional subtypes may exist. We have identified two novel genes, which encode candidate PBPs (BmorPBP2, BmorPBP3). Comparison with PBPs from various moth species have revealed a high degree of sequence identity and the three BmorPBP-subtypes can be assigned to distinct groups within the moth PBP family. In situ hybridization revealed that BmorPBP2 and BmorPBP3 are expressed only in relatively few cells compared to the number of cells expressing BmorPBP1. Double-labeling experiments have shown that the two novel BmorPBPs are expressed in the same cells but are not co-expressed with BmorPBP1. Furthermore, unlike BmorPBP1, cells expressing the newly identified PBPs did not surround neurons containing the BmOR-1 receptor. The results indicate that BmorPBP2 and BmorPBP3 are located in sensilla types, which are different from the long sensilla trichodea.

A Conserved Subtilisin Protease Identified in Babesia divergens Merozoites

Invasion of erythrocytes is an integral part of the Babesia divergens life cycle. Serine proteases have been shown to play an important role in invasion by related Apicomplexan parasites such as the malaria parasite Plasmodium falciparum. Here we demonstrate the presence of two dominant serine proteases in asexual B. divergens using a biotinylated fluorophosphonate probe. One of these active serine proteases (p48) and its precursors were recognized by anti-PfSUB1 antibodies. These antibodies were used to clone the gene encoding a serine protease using a B. divergens cDNA library. BdSub-1 is a single copy gene with no introns. The deduced gene product (BdSUB-1) clearly belongs to the subtilisin superfamily and shows significant homology to Plasmodium subtilisins, with the highest degree of sequence identity around the four catalytic residues. Like subtilisin proteases in other Apicomplexan parasites, BdSUB-1 undergoes two steps of processing during activation in the secretory pathway being finally converted to an active form (p48). The mature protease is concentrated in merozoite dense granules, apical secretory organelles involved in erythrocyte invasion. Anti-PfSUB1 antibodies have a potent inhibitory effect on erythrocyte invasion by B. divergens merozoites in vitro. This report demonstrates conservation of the molecular machinery involved in erythrocyte invasion by these two Apicomplexan parasites and paves the way for a comparative analysis of other molecules that participate in this process in the two parasites.

A mutation in anexbDgene reduces tagetitoxin production byPseudomonas syringaepv.tagetis

A mutant of Pseudomonas syringae pv. tagetis EB037 with limited ability to produce tagetitoxin was isolated after transposon mutagenesis and the mutation was characterized. The mutation occurred in a gene with a high degree of sequence identity to exbD. exbD is contiguous with tonB and exbB upstream and with a gene for a TonB-dependent receptor downstream. Using reverse transcription - polymerase chain reaction with RNA from the wild-type and exbD mutant strains, we demonstrated that the mutation in exbD did not have a polar affect on the expression of downstream genes. The exbD mutant was able to grow well in conditions where iron is not freely available. Siderophore production by the exbD mutant was similar to that of the wild-type strain. We conclude that the mutation in exbD disrupts tagetitoxin production without compromising iron metabolism. The results indicate that tagetitoxin export by P. syringae pv. tagetis involves an efflux pump that requires a functional TonB system that is not essential for normal iron metabolism.

Large-Scale Predictions of Gram-Negative Bacterial Protein Subcellular Locations

Many species of Gram-negative bacteria are pathogenic bacteria that can cause disease in a host organism. This pathogenic capability is usually associated with certain components in Gram-negative cells. Therefore, developing an automated method for fast and reliable prediction of Gram-negative protein subcellular location will allow us to not only timely annotate gene products, but also screen candidates for drug discovery. However, protein subcellular location prediction is a very difficult problem, particularly when more location sites need to be involved and when unknown query proteins do not have significant homology to proteins of known subcellular locations. PSORT-B, a recently updated version of PSORT, widely used for predicting Gram-negative protein subcellular location, only covers five location sites. Also, the data set used to train PSORT-B contains many proteins with high degrees of sequence identity in a same location group and, hence, may bear a strong homology bias. To overcome these problems, a new predictor, called "Gneg-PLoc", is developed. Featured by fusing many basic classifiers each being trained with a stringent data set containing proteins with strictly less than 25% sequence identity to one another in a same location group, the new predictor can cover eight subcellular locations; that is, cytoplasm, extracellular space, fimbrium, flagellum, inner membrane, nucleoid, outer membrane, and periplasm. In comparison with PSORT-B, the new predictor not only covers more subcellular locations, but also yields remarkably higher success rates. Gneg-PLoc is available as a Web server at http://202.120.37.186/bioinf/Gneg. To support the demand of people working in the relevant areas, a downloadable file is provided at the same Web site to list the results identified by Gneg-PLoc for 49 907 Gram-negative protein entries in the Swiss-Prot database that have no subcellular location annotations or are annotated with uncertain terms. The large-scale results will be updated twice a year to cover the new entries of Gram-negative bacterial proteins and reflect the new development of Gneg-PLoc.

Phylogenetic Analysis of Anaplasma marginale Strains from Paraná State, Brazil, Using the msp1α and msp4 genes

Anaplasma marginale is an obligate intraerythrocytic rickettsial pathogen (order, Rickettsiales: family, Anaplasmataceae) that causes bovine anaplasmosis. This disease is widely distributed in tropical and sub-tropical regions of the world and causes important economic losses to cattle production. Major surface protein (MSP)1a (msp1alpha gene) is one of the six MSPs identified on A. marginale from cattle, whose sequence and size vary according to the number of tandem 28- to 29-amino acid repeats. This study characterized the msp1alpha and msp4 genes obtained from three distinct Brazilian herds from the State of Paraná. Three strains of the msp1alpha and one strain of the msp4 gene were sequenced. The strains evaluated revealed PCR products of different size, representing three, five and six internal repeats. Sequence analyses confirmed the number of tandem sequence copies and revealed a high degree of sequence identity with strains from other Brazilian States, as well as strains from the USA, Europe and Israel. The msp1alpha DNA and amino acid sequences from A. marginale and DNA sequences of msp4 strains did not reveal distinct phylogeographical segregation. However, the amino acid sequences of msp4 demonstrated definite phylogeographical relationship. These results suggest that the amino acid sequences of msp4 should be used for phylogenetic identification of A. marginale strains and may be an important tool for the epidemiology and control of anaplasmosis. Additionally, the close similarity of the Paraná strains of A. marginale with strains from USA, Europe and Asia may reflect the introduction of these genes during the development of the Brazilian bovine herd.

Mutation of fungal endoglucanases into glycosynthases and characterization of their acceptor substrate specificity

Humicola insolens mutant Cel7B E197A is a powerful endo-glycosynthase displaying an acceptor substrate specificity restricted to β- d-glucosyl, β- d-xylosyl, β- d-mannosyl and β- d-glucosaminyl in +1 subsite. Our aim was to extend this substrate specificity to β- d- N-acetylglucosaminyl, in order to get access to a wider array of oligosaccharidic structures obtained through glycosynthase assisted synthesis. In a first approach a trisaccharide bearing a β- d- N-acetylglucosaminyl residue was docked at the +1 subsite of H. insolens Cel7B, indicating that the mutation of only one residue, His209, could lead to the expected wider acceptor specificity. Three H. insolens Cel7B glycosynthase mutants (H209A, H209G and H209A/A211T) were produced and expressed in Aspergillus oryzae. In parallel, sequence alignment investigations showed that several cellulases from family GH7 display an alanine residue instead of histidine at position 209. Amongst them, Trichoderma reesei Cel7B, an endoglucanase sharing the highest degree of sequence identity with Humicola Cel7B, was found to naturally accept a β- d- N-acetylglucosaminyl residue at +1 subsite. The T. reesei Cel7B mutant nucleophile E196A was produced and expressed in Saccharomyces cerevisiae, and its activity as glycosynthase, together with the H. insolens glycosynthase mutants, was evaluated toward various glycosidic acceptors.

Atypical Haemolytic Uraemic Syndrome Associated with a Hybrid Complement Gene

BackgroundSequence analysis of the regulators of complement activation (RCA) cluster of genes at chromosome position 1q32 shows evidence of several large genomic duplications. These duplications have resulted in a high degree of sequence identity between the gene for factor H (CFH) and the genes for the five factor H-related proteins (CFHL1–5; aliases CFHR1–5). CFH mutations have been described in association with atypical haemolytic uraemic syndrome (aHUS). The majority of the mutations are missense changes that cluster in the C-terminal region and impair the ability of factor H to regulate surface-bound C3b. Some have arisen as a result of gene conversion between CFH and CFHL1. In this study we tested the hypothesis that nonallelic homologous recombination between low-copy repeats in the RCA cluster could result in the formation of a hybrid CFH/CFHL1 gene that predisposes to the development of aHUS.Methods and FindingsIn a family with many cases of aHUS that segregate with the RCA cluster we used cDNA analysis, gene sequencing, and Southern blotting to show that affected individuals carry a heterozygous CFH/CFHL1 hybrid gene in which exons 1–21 are derived from CFH and exons 22/23 from CFHL1. This hybrid encodes a protein product identical to a functionally significant CFH mutant (c.3572C>T, S1191L and c.3590T>C, V1197A) that has been previously described in association with aHUS.Conclusions CFH mutation screening is recommended in all aHUS patients prior to renal transplantation because of the high risk of disease recurrence post-transplant in those known to have a CFH mutation. Because of our finding it will be necessary to implement additional screening strategies that will detect a hybrid CFH/CFHL1 gene.

Molecular Characterization of the Recombinant A-chain of a Type II Ribosome-Inactivating Protein (RIP) from Viscum album coloratum and Structural Basis on its Ribosome-Inactivating Activity and the Sugar-binding Properties of the B-chain

Mistletoe (Viscum album) lectins, which are classified as a type II ribosome-inactivating protein (RIP) due to their unique biological function and the potential medical and therapeutic application in cancer cells, receive a rising attention. The heterodimeric glycoproteins contain the Achain with catalytic activity and the B-chain with sugar binding properties. In recent years, studies involving the lectins from the white berry European mistletoe (Viscum album) and the yellow berry Korean mistletoe (Viscum album coloratum) have been described. However, the detailed mechanism in exerting unique cytotoxic effect on cancer cells still remains unclear. Here, we aim to understand and define the molecular basis and biological effects of the type II RIPs, through the studies of the recombinant Korean mistletoe lectin. To this end, we expressed, purified the recombinant Korean mistletoe lectin (rKML), and investigated its molecular characteristics in vitro, its cytotoxicity and ability to induce apoptotic cell death in cancer cells. To gain structural basis for its catalytic activity and sugar binding properties, we performed homology modeling studies based on the high degree of sequence identity and conserved secondary structure prediction between Korean and European, Himalayan mistletoe lectins, and Ricin.

Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes.

Previous studies with human and bacterial topoisomerases suggest that the type II enzyme utilizes two distinct mechanisms to recognize the handedness of DNA supercoils. It has been proposed that the ability of some type II enzymes, such as human topoisomerase IIalpha and Escherichia coli topoisomerase IV, to distinguish supercoil geometry during DNA relaxation is mediated by elements in the variable C-terminal domain of the protein. In contrast, the ability of human topoisomerase IIalpha and topoisomerase IIbeta to discern the handedness of supercoils during DNA cleavage suggests that residues in the conserved N-terminal or central domain of the protein are involved in this process. To test this hypothesis, the ability of Paramecium bursaria chlorella virus-1 (PBCV-1) and chlorella virus Marburg-1 (CVM-1) topoisomerase II to relax and cleave negatively and positively supercoiled plasmids was assessed. These enzymes display a high degree of sequence identity with the N-terminal and central domains of eukaryotic topoisomerase II but naturally lack the C-terminal domain. While PBCV-1 and CVM-1 topoisomerase II relaxed under- and overwound substrates at similar rates, they were able to discern the handedness of supercoils during the cleavage reaction and preferentially cut negatively supercoiled DNA. Preferential cleavage was not due to a change in site specificity, DNA binding, or religation. These findings are consistent with a bimodal recognition of DNA geometry in which topoisomerase II uses elements in the C-terminal domain to sense the handedness of supercoils during DNA relaxation and elements in the conserved N-terminal or central domain during DNA cleavage.

Isolation and characterization of a coronavirus from pigeons with pancreatitis

To identify and partially characterize a coronaviruslike virus isolated from naturally infected pigeons. 50 specific pathogen-free (SPF) embryonated chicken eggs, 30 White Leghorn SPF chickens, and 12 clinically normal pigeons. Pancreatic tissue specimens from sick pigeons were inoculated into SPF embryonated chicken eggs for viral isolation and investigation of morphologic and hemagglutinating properties of the isolate, called PSH050513. Furthermore, virulence studies in SPF chickens and experimental pigeons were performed. The spike (S) glycoprotein gene of PSH050513 was further sequenced and analyzed. PSH050513 was isolated and identified from the experimentally infected pigeons by a routine method, which was in accordance with Koch's postulates. The complete S protein (1,167 amino acids) was compared with published S protein sequences of other avian and mammalian coronaviruses. A high degree of sequence identity (79.3% to 99.6%) was observed between the S protein sequence of PSH050513 and published sequences of avian infectious bronchitis virus (IBV); only limited identity (< 37.8%) was observed with turkey coronavirus and mammalian coronaviruses. Furthermore, when the virus was inoculated into SPF chickens, pancreatitis developed. PSH050513 has been tentatively identified as a novel member of group 3 coronaviruses that have close genetic relationships with IBV strains.

The Killer Immunoglobulin-Like Receptor Gene Cluster: Tuning the Genome for Defense

Killer immunoglobulin-like receptors (KIRs) are molecules expressed on the surface of natural killer (NK) cells, which play an important role in innate immunity. KIR recognition of major histocompatability complex (MHC) class I allotypes represents one component of the complex interactions between NK cells and their targets in determining NK cell reactivity. KIRs are encoded by a gene cluster at human chromosome 19q13.4. Despite their high degree of sequence identity, KIR genes encode proteins that have diverse recognition patterns (specific HLA class I allotypes) and confer opposing signals (activating or inhibitory) to the NK cell. The KIR gene cluster is highly polymorphic, with individual genes exhibiting allelic variability and individual haplotypes differing in gene content. The polymorphism of the KIR locus parallels that of the MHC, facilitating the adaptation of the immune system to a dynamic, challenging environment. This variation is associated with a growing number of human diseases, which is likely to extend to levels observed for the HLA loci. Here we review current progress in understanding KIR biology and genetics.

Structure of 8Sα globulin, the major seed storage protein of mung bean

The 8S globulins of mung bean [Vigna radiata (L.) Wilczek] are vicilin-type seed storage globulins which consist of three isoforms: 8Salpha, 8Salpha' and 8Sbeta. The three isoforms have high sequence identities with each other (around 90%). The structure of 8Salpha globulin has been determined for the first time by X-ray crystallographic analysis and refined at 2.65 A resolution with a final R factor of 19.6% for 10-2.65 A resolution data. The refined 8Salpha globulin structure consisted of 366 of the 423 amino-acid residues (one subunit of the biological trimer). With the exception of several disordered regions, the overall 8Salpha globulin structure closely resembled those of other seed storage 7S globulins. The 8Salpha globulin exhibited the highest degree of sequence identity (68%) and structural similarity (a root-mean-square deviation of 0.6 A) with soybean beta-conglycinin beta (7S globulin). Their surface hydrophobicities are also similar to each other, although their solubilities differ under alkaline conditions at low ionic strength. This difference seems to be a consequence of charge-charge interactions and not hydrophobic interactions of the surfaces, based on a comparison of the electrostatic potentials of the molecular surfaces. The thermal stability of 8Salpha globulin is lower than that of soybean beta-conglycinin beta. This correlates with the cavity size derived from the crystal structure, although other structural features also have a small effect on the protein's thermal stability.