Determinants of host specificity and comments on attachment site specificity of tetraphyllidean cestodes infecting rajid skates from the northwest Atlantic

The objectives of this study were to (1) describe the host range for 6 tetraphyllidean species and quantify their host specificity using 5 specificity indices; (2) determine the role of morphological determinants in the host specificity of tetraphyllideans by comparing villar and bothridial measurements of species examined herein; and (3) determine the role of a physiological component in the host specificity of tetraphyllideans by exposing tetraphyllideans to blood sera from different fish species and other solutions. Our results indicate that Echeneibothrium dubium abyssorum (ex Amblyraja radiata), Echeneibothrium canadensis (ex A. radiata), and Zyxibothrium kamienae (ex Malacoraja senta) exhibit the highest degree of specificity, followed by Echeneibothrium vernetae (ex Leucoraja erinacea and Leucoraja ocellata), Pseudanthobothrium hanseni (ex A. radiata and M. senta), and Pseudanthobothrium purtoni (ex Leucoraja erinacea and L. ocellata). However, these results vary based on the specificity index used. Compatible bothridial and villar measurements indicate that there is no morphological determinant of host specificity but that there is a morphological determinant to attachment site specificity. Our data indicate that attachment site specificity may also be phylogenetically determined. Additionally, the exposure of parasites to blood sera from various hosts confirms that host specificity in this system has a physiological determinant. Therefore, host specificity in this system is determined, at least in part, by physiological factors, whereas attachment site specificity is an extension of host specificity and is phylogenetically determined.     

Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction

Microarray-hybridization specificity is one of the main effectors of microarray result quality. In the present review, we suggest a definition for specificity that spans four hybridization levels, from the single probe to the microarray platform. For increased hybridization specificity, it is important to quantify the extent of the specificity at each of these levels, and correct the data accordingly. We outline possible effects of low hybridization specificity on the obtained results and list possible effectors of hybridization specificity. In addition, we discuss several studies in which theoretical approaches, empirical means or data filtration were used to identify specificity effectors, and increase the specificity of the hybridization results. However, these various approaches may not yet provide an ultimate solution; rather, further tool development is needed to enhance microarray-hybridization specificity.     

Can extinction risk help explain plant–pollinator specificity among euglossine bee pollinated plants?

Long‐term or lifetime specificity in plant–pollinator relationships is likely a consequence of natural selection to not only enhance the probability of cross‐pollination but also to improve pollinator efficiency. Dependency on one or few pollinators involves risk whereas multiple species may reduce the probability of extinction via unreliable pollinator service. We analyzed specificity in terms of factors that may ameliorate risk such as long‐term pollinator population stability, abundance and the duration of flowering. Bee population stability indices from seven continuous years of census data, combined with pollinator and flowering phenology data for 37 plant species in Panama, revealed pollinator specificity was not related to pollinator population stability. No relationship existed between the length of a flowering season and population stability of associated pollinators. Further data from 30 years of euglossine monitoring also revealed no relationship between bee abundance and specificity. However, a strong relationship was revealed between length of flowering period and specificity. A longer flowering season was associated with lower specificity and shorter flowering was associated with higher specificity, which is as expected if specificity is the outcome of a sampling problem but not as expected if specificity is accompanied by risk reduction. Plant–pollinator specificity involving euglossine bees is evidently not related to bee population stability, abundance, or length of flowering period, in a manner that we predicted would be associated with reducing the risk of extinction. Variation in population stabilities of euglossines may be insufficient to be a factor in the evolution of plant–pollinator specificity. In the tropics, specificity may be more associated with plant longevity, selection for efficiency or effectiveness, or flowering duration –as a sampling phenomenon, than with reducing dependence on unreliable pollinators.     

Changing the substrate specificity of creatine kinase from creatine to glycocyamine: evidence for a highly evolved active site

Eight variants of creatine kinase were created to switch the substrate specificity from creatine to glycocyamine using a rational design approach. Changes to creatine kinase involved altering several residues on the flexible loops that fold over the bound substrates including a chimeric replacement of the guanidino specificity loop from glycocyamine kinase into creatine kinase. A maximal 2,000-fold change in substrate specificity was obtained as measured by a ratio of enzymatic efficiency (k(cat)/K(M).K(d)) for creatine vs. glycocyamine. In all cases, a change in specificity was accompanied by a large drop in enzymatic efficiency. This data, combined with evidence from other studies, indicate that substrate specificity in the phosphagen kinase family is obtained by precise alignment of substrates in the active site to maximize k(cat)/K(M).K(d) as opposed to selective molecular recognition of one guanidino substrate over another. A model for the evolution of the dimeric forms of phosphagen kinases is proposed in which these enzymes radiated from a common ancestor that may have possessed a level of catalytic promiscuity. As mutational events occurred leading to greater degrees of substrate specificity, the dimeric phosphagen kinases became evolutionary separated such that the substrate specificity could not be interchanged by a small number of mutations.     

Geographical variation in host specificity of fleas (Siphonaptera) parasitic on small mammals: the influence of phylogeny and local environmental conditions

The evolution of host specificity remains a central issue in the study of host‐parasite relationships. Here we tackle three basic questions about host specificity using data on host use by fleas (Siphonaptera) from 21 geographical regions. First, are the host species exploited by a flea species no more than a random draw from the locally available host species, or do they form a taxonomically distinct subset? Using randomization tests, we showed that in the majority of cases, the taxonomic distinctness (measured as the average taxonomic distances among host species) of the hosts exploited by a flea is no different from that of random subsets of hosts taken from the regional pool. In the several cases where a difference was found, the taxonomic distinctness of the hosts used by a flea was almost always lower than that of the random subsets, suggesting that the parasites use hosts within a narrower taxonomic spectrum than what is available to them. Second, given the variation in host specificity among populations of the same flea species, is host specificity truly a species character? We found that host specificity measures are repeatable among different populations of the same flea species: host specificity varies significantly more among flea species than within flea species. This was true for both measures of host specificity used in the analyses: the number of host species exploited, and the index measuring the average taxonomic distinctness of the host species and its variance. Third, what causes geographical variation in host specificity among populations of the same flea species? In the vast majority of flea species, neither of our two measures of host specificity correlated with either the regional number of potential host species or their taxonomic distinctness, or the distance between the sampled region and the center of the flea's geographical range. However, in most flea species host specificity correlated with measures of the deviation in climatic conditions (precipitation and temperature) between the sampled region and the average conditions computed across the flea's entire range. Overall, these results suggest that host specificity in fleas is to a large extent phylogenetically constrained, while still strongly influenced by local environmental conditions.     

Host specificity determinants as a genetic continuum

Host specificity is an important concept that underlies the interaction of all clinically and agriculturally relevant microbes with their hosts. Changes in the host specificity of animal pathogens, in particular, are often of greatest concern due to their immediate and unexpected impact on human health. Host switching or host jumps can often be traced to modification of key microbial pathogenicity factors that facilitate the formation of particular host associations. An increase in the number of genome-level studies has begun revealing that almost any type of change, from the simplest to the most complex, can potentially impact host specificity. This review highlights examples of host specificity determinants of viruses, bacteria and fungi, and presents them from within a genetic continuum that spans from the single residue through to entire genomic islands.     

Current trends of lectins from microfungi

Lectins are widespread in nature and have been isolated from plants, animals, microorganisms, and viruses. Although several lectins have been reported from microfungi, many more genera still remain unexplored and their physiological role is also uncertain. Microfungal lectins show wide disparity regarding their specificity to erythrocytes. Only a few lectins display specificity to particular human blood types. In addition, they also show agglutination to various animal erythrocytes. Many lectins from microfungi exhibit stringent specificity to animal glycoproteins, while a few have much more simplified sugar binding properties. The role of few microfungal lectins in host-parasite interactions, as storage proteins, and in growth and morphogenesis has been proposed. The current review focuses on an overview of lectins from microfungi, their specificity towards erythrocytes and carbohydrates, physicochemical characteristics, and their possible role and applications.     

Current trends of lectins from microfungi

Lectins are widespread in nature and have been isolated from plants, animals, microorganisms, and viruses. Although several lectins have been reported from microfungi, many more genera still remain unexplored and their physiological role is also uncertain. Microfungal lectins show wide disparity regarding their specificity to erythrocytes. Only a few lectins display specificity to particular human blood types. In addition, they also show agglutination to various animal erythrocytes. Many lectins from microfungi exhibit stringent specificity to animal glycoproteins, while a few have much more simplified sugar binding properties. The role of few microfungal lectins in host-parasite interactions, as storage proteins, and in growth and morphogenesis has been proposed. The current review focuses on an overview of lectins from microfungi, their specificity towards erythrocytes and carbohydrates, physicochemical characteristics, and their possible role and applications.     

Catalytic competence of human alpha- and gamma-thrombin in the activation of fibrinogen and factor XIII

Steady-state kinetic parameters were compared for the action of alpha- and gamma-thrombin on the physiologically important thrombin substrates fibrinogen and factor XIII at 37 degrees C, pH 7.4, and 0.14 M NaCl. gamma-Thrombin, an alpha-thrombin derivative proteolytically cleaved at R-B73 and K-B154, was observed to catalyze the release of fibrinopeptide A (FPA) from fibrinogen with a specificity constant (kcat/Km) of 5 X 10(3) M-1 s-1. This value was approximately 2400-fold lower than the specificity constant for the corresponding alpha-thrombin-catalyzed reaction. The low specificity constant was attributed to an increase in Km and a decrease in kcat for gamma-thrombin-catalyzed release of FPA from fibrinogen. Conversion of alpha-thrombin to gamma-thrombin also resulted in an approximately 800-fold reduction in the specificity constant for thrombin-catalyzed release of fibrinopeptide B (FPB) from fibrin I, as well as a loss in discriminatory power. Whereas alpha-thrombin preferentially released FPA from intact fibrinogen, gamma-thrombin released FPA and FPB from intact fibrinogen at similar rates. In contrast to the large difference in specificity constants observed for alpha- and gamma-thrombin catalysis with fibrin(ogen) as substrate, the specificity constant (2.6 X 10(4) M-1 s-1) observed for gamma-thrombin-catalyzed release of activation peptide from factor XIII was only 5-fold lower than the corresponding value for the alpha-thrombin-catalyzed reaction. Additionally, the promotion of factor XIII activation by fibrin characteristic of the alpha-thrombin-catalyzed reaction did not occur in the gamma-thrombin-catalyzed reaction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Natural variation at position 45 in the D1 domain of lineage III killer cell immunoglobulin-like receptors (KIR) has major effects on the avidity and specificity for MHC class I

Alternative lysine and methionine residues at position 44 in the D1 domain determine the specificities of human lineage III killer cell immunoglobulin-like receptors (KIR) for the C1 and C2 epitopes of HLA-C. KIR having glutamate 44 are also present in orangutans (Popy2DLB) and chimpanzees (Pt-2DL9) but notably absent from humans. Popy2DLB exhibits broad specificity for both the C1 and C2 epitopes, whereas Pt-2DL9 has narrow specificity for C2. Mutation of phenylalanine 45 in Popy2DLB to the cysteine residue present in Pt-2DL9 was sufficient to narrow the Popy2DLB specificity to be like that of Pt-2DL9. In contrast, replacement of cysteine 45 in Pt-2DL9 by phenylalanine had no effect on its C2 specificity, but reduced the avidity. In a similar manner, replacement of phenylalanine 45 with cysteine in Popy2DLA, which has lysine 44 and recognizes C1, maintained this specificity while reducing avidity. Position 45 is exceptionally variable, exhibiting twelve residues that distinguish KIR of different lineages and species. Our study demonstrates the potential for variation at position 45 to modulate KIR avidity and specificity for HLA-C. The various effects of position 45 mutation are consistent with a model in which a Popy2DLB-like receptor, having glutamate 44 and broad specificity for C1 and C2, facilitated the evolution of the C2 epitope from the C1 epitope and C2-specific KIR from C1-specific KIR. With the acquisition of C2 and C2-specific receptors, the selection against this broadly specific receptor led to its loss from the human line and narrowing of its specificity on the chimpanzee line.     

Specificity of cleavage by restriction nuclease from Bacillus subtilis.

The restriction nuclease from B. subtilis (Bsu) which cleaves in the middle of the tetra-nucleotide sequence 5'-GGCC-3' 3'-CCGG-5' has been found to decrease its substrate specificity at high nuclease concentrations. There are special conditions, high pH, low ionic strength, and high glycerol content, which strongly enhance splitting with decreased specificity and also lead to splitting of single-stranded DNA. By sequence analyses it is shown that the reduction in specificity of Bsu corresponds to cleavage predominantly at 5'-GC-3' 3'-CG-5' sequences. No comparable change in specificity has been observed in a restriction nuclease from Haemophilus aegyptius (HaeIII), and isoschizomer of Bsu.     

Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites

Proteomic identification of protease cleavage site specificity (PICS) is a recent proteomic approach for the easy mapping of protease subsite preferences that determines both the prime- and non-prime side specificity concurrently. Here we greatly facilitate user access by providing an automated and simple web-based data-analysis resource termed WebPics (http://clipserve.clip.ubc.ca/pics/). We demonstrate the utility of WebPics analysis of PICS data by determining the substrate specificity of factor Xa from P6-P6', an important blood coagulation protease that proteolytically generates thrombin from prothrombin. PICS confirms existing data on non-prime site specificity and refines our knowledge of factor Xa prime-site selectivity.     

Host-parasitoid association and diffuse coevolution: when to be a generalist?

In host-parasitoid communities, hosts are subjected to selective pressures from numerous parasitoid species, and parasitoids may attack several host species. The specificity of host resistance and parasitoid virulence is thus a key factor in host-parasitoid coevolution. A continuum of strategies exists, from strict specificity to a generalist strategy. The optimal level of specificity may differ in host and parasitoid. I investigated the optimal level of resistance specificity using a model in which the host could be attacked by two parasitoid species, with variable levels of defense specificity. The fitness of a parasitoid attacking two host species with different levels of virulence specificity was also modeled. Finally, a fluctuating environment was simulated by introducing variable probabilities of encounters between antagonistic species over several generations. If the frequency of encounters with the antagonistic species is fixed, then both host and parasitoid gain from a strategy of exclusive specialization toward the most frequent antagonist. If the frequency of encounters fluctuates between generations, generalist host resistance and partially specialist parasitoid virulence are favored. Generalist host resistance may be considered to be a bet-hedging response to an unpredictable environment. This asymmetry in host-parasitoid coevolution may account for some of the genetic structures observed in the field for host-parasitoid associations.     

Biochemical studies of taste sensation--XII. Specificity of binding of taste ligands to a sedimentable fraction from catfish taste tissue

The specificity of amino acid binding sites in a sedimentable fraction prepared from catfish taste epithelium was examined. Using seven 3H-labeled amino acids as ligands and the unlabeled amino acids in binding competition assays, the presence of possibly three classes of amino acid binding sites was deduced. Site 1 binds L-THR, L-SER, L-ALA and possibly D-ALA and beta-ALA, Site 2 binds L-SER, L-ALA, GLY, D-ALA, and beta-ALA and Site 3 binds L-ARG and L-LYS. Additional evidence supporting the specificity of Site 2 was obtained from the specificity of enhancement of L-ALA binding. The results demonstrate the presence of some major classes of taste receptor sites, and provide a basis for understanding taste receptor specificity at the biochemical level.     

Comparison of the lectin-like activity of pertussis toxin with two plant lectins that have differential specificities for alpha (2-6) and alpha (2-3)-linked sialic acid

In this report we have compared the lectin-like properties of Pertussis toxin with two plant lectins which are known to possess different specificities towards terminal Neu5Ac Gal linkages on glycoconjugates. The hemagglutinin from elderberry bark (Sambucus nigra) has a binding specificity for terminal Neu5Ac alpha (2-6) Gal sequences and was found to bind a series of glycoconjugates with a similar specificity as Pertussis toxin. The binding specificity of Pertussis toxin was different from that of the leukoagglutinin from the seeds of Maackia amurensis which preferentially binds terminal Neu5Ac alpha (2-3) Gal sequences. These observations confirm the specificity of Pertussis toxin for Neu5Ac alpha (2-6) Gal glycoconjugate sequences.     

Using substrate engineering to harness enzymatic promiscuity and expand biological catalysis

Despite their unparalleled catalytic prowess and environmental compatibility, enzymes have yet to see widespread application in synthetic chemistry. This lack of application and the resulting underuse of their enormous potential stems not only from a wariness about aqueous biological catalysis on the part of the typical synthetic chemist but also from limitations on enzyme applicability that arise from the high degree of substrate specificity possessed by most enzymes. This latter perceived limitation is being successfully challenged through rational protein engineering and directed evolution efforts to alter substrate specificity. However, such programs require considerable effort to establish. Here we report an alternative strategy for expanding the substrate specificity, and therefore the synthetic utility, of a given enzyme through a process of "substrate engineering". The attachment of a readily removable functional group to an alternative glycosyltransferase substrate induces a productive binding mode, facilitating rational control of substrate specificity and regioselectivity using wild-type enzymes.     

Structural determinants and distribution of phosphate specificity in ribonucleotide reductases

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. RNRs are specific for either ribonucleoside diphosphates or triphosphates as substrates. As far as is known, oxygen-dependent class I RNRs (NrdAB) all reduce ribonucleoside diphosphates, and oxygen-sensitive class III RNRs (NrdD) are all ribonucleoside triphosphate reducers, whereas the adenosylcobalamin-dependent class II (NrdJ) contains both ribonucleoside diphosphate and triphosphate reducers. However, it is unknown how this specificity is conveyed by the active site of the enzymes and how this feature developed in RNR evolution. By structural comparison of the active sites in different RNRs, we identified the apical loop of the phosphate-binding site as a potential structural determinant of substrate specificity. Grafting two residues from this loop from a diphosphate- to a triphosphate-specific RNR caused a change in preference from ribonucleoside triphosphate to diphosphate substrates in a class II model enzyme, confirming them as the structural determinants of phosphate specificity. The investigation of the phylogenetic distribution of this motif in class II RNRs yielded a likely monophyletic clade with the diphosphate-defining motif. This indicates a single evolutionary-split event early in NrdJ evolution in which diphosphate specificity developed from the earlier triphosphate specificity. For those interesting cases where organisms contain more than one nrdJ gene, we observed a preference for encoding enzymes with diverse phosphate specificities, suggesting that this varying phosphate specificity confers a selective advantage.     

Photolabelling the urotensin II receptor reveals distinct agonist- and partial-agonist-binding sites

A re-investigation of the occurrence and taxonomic distribution of proteins built up of protomers consisting of two tandem arrayed domains equivalent to the GNA [Galanthus nivalis (snowdrop) agglutinin] revealed that these are widespread among monotyledonous plants. Phylogenetic analysis of the available sequences indicated that these proteins do not represent a monophylogenetic group but most probably result from multiple independent domain duplication/in tandem insertion events. To corroborate the relationship between inter-domain sequence divergence and the widening of specificity range, a detailed comparative analysis was made of the sequences and specificity of a set of two-domain GNA-related lectins. Glycan microarray analyses, frontal affinity chromatography and surface plasmon resonance measurements demonstrated that the two-domain GNA-related lectins acquired a marked diversity in carbohydrate-binding specificity that strikingly contrasts the canonical exclusive specificity of their single domain counterparts towards mannose. Moreover, it appears that most two-domain GNA-related lectins interact with both high mannose and complex N-glycans and that this dual specificity relies on the simultaneous presence of at least two different independently acting binding sites. The combined phylogenetic, specificity and structural data strongly suggest that plants used domain duplication followed by divergent evolution as a mechanism to generate multispecific lectins from a single mannose-binding domain. Taking into account that the shift in specificity of some binding sites from high mannose to complex type N-glycans implies that the two-domain GNA-related lectins are primarily directed against typical animal glycans, it is tempting to speculate that plants developed two-domain GNA-related lectins for defence purposes.     

Glucocorticoid-specific gene activation by the intact human glucocorticoid receptor expressed in yeast. Glucocorticoid specificity depends on low level receptor expression.

In the presence of appropriate reporter genes mammalian nuclear receptors are competent to transactivate gene expression when expressed in yeast cells. Thus yeast genetics could be used to identify determinants of steroid specificity for these mammalian proteins. However, unlike the estrogen, progesterone, vitamin D3, and thyroid hormone receptors, the glucocorticoid receptor shows an apparently abnormal steroid specificity in yeast (Schena, M., and Yamamoto, K. (1988) Science 241, 965-967), suggesting that the expressed protein might be incorrectly folded. We show here that the glucocorticoid receptor does exhibit a normal steroid specificity in yeast cells, but only at low levels of expressed receptor protein. Thus, at least under these conditions, genetic studies on steroid specificity are possible. At least part of the abnormal specificity that is sometimes observed for the glucocorticoid receptor in yeast appears to result from an artifact of the assay system and is not due to an abnormal receptor structure. This mechanism could account for all our data and so could provide the sole explanation of the abnormal specificity observed. However, it is also possible that part of the abnormal specificity could result from structural or other changes in receptor function, which occur when the receptor expression level is increased.