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PubMed2005

Molecular evidence confirms multiple origins of aquatic hyphomycetes.

Traditional taxonomy of aquatic hyphomycetes has been based on conidial morphology and development. Since the predominantly tetraradiate and sigmoid forms are due to convergent evolution, they are often phylogenetically non-informative. The comparison of nuclear small-subunit ribosomal DNA sequences of 30 species (22 new, eight previously published) assigned 22 to Leotiomycetes, four to Dothideomycetes, three to Sordariomycetes, and one to Orbiliomycetes. Eight species of Anguillospora were distributed among the Leotiomycetes, Dothideomycetes, and Orbiliomycetes. All three anamorphs connected with Massarina were assigned to the Pleosporales, however, Clavariopsis aquatica and Tumularia aquatica separated from Anguillospora longissima. The nSSU rDNA sequences of several species were identical (e.g. Anguillospora crassa and A. furtiva), suggesting the need to include less conservative genes for resolving such differences.

Ascomycota↗
PubMed1995

Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity.

The three-dimensional structure of D-amino acid aminotransferase (D-AAT) in the pyridoxamine phosphate form has been determined crystallographically. The fold of this pyridoxal phosphate (PLP)-containing enzyme is completely different from those of any of the other enzymes that utilize PLP as part of their mechanism and whose structures are known. However, there are some striking similarities between the active sites of D-AAT and the corresponding enzyme that transaminates L-amino acids, L-aspartate aminotransferase. These similarities represent convergent evolution to a common solution of the problem of enforcing transamination chemistry on the PLP cofactor. Implications of these similarities are discussed in terms of their possible roles in the stabilization of intermediates of a transamination reaction. In addition, sequence similarity between D-AAT and branched chain L-amino acid aminotransferase suggests that this latter enzyme will also have a fold similar to that of D-AAT.

Alanine Transaminase↗
PubMed1993

Folding of subtilisin BPN': characterization of a folding intermediate.

Subtilisin BPN', an extracellular serine protease from Bacillus amyloliquefaciens, requires a 77 amino acid pro-sequence for correct folding in vivo. We report the observation of a metastable folding intermediate during the refolding of wild-type and a proteolytically inactive mutant subtilisin BPN' that lack the pro-sequence. The addition of the pro-sequence as a separate polypeptide chain results in the folding of the intermediate to the native state. The intermediate state of subtilisin is stable at different temperatures, pH values, and salt concentrations for more than a week and retains its competence for folding. The intermediate state possesses a compactness between that of the native and unfolded states. Although it has native-like secondary structure, it shows no distinct near-UV CD spectrum and has a strongly reduced dispersion in the amide and methyl regions of the 1H NMR spectrum. These indicate considerably less tertiary structure than possessed by the native state. However, the intermediate conformation has regions of stable tertiary structure: it has a high-affinity calcium binding site and, after a first noncooperative transition, unfolds with guanidinium chloride in a cooperative process. These results support a folding mechanism for subtilisin BPN' that comprises a high energy transition state, which is lowered by the interaction with the pro-sequence. The similarity to the folding mechanism of alpha-lytic protease supports the hypothesis that a common folding mechanism has been developed through convergent evolution.

Amino Acid Sequence↗
PubMed2000

The active site structure of Thalassiosira weissflogii carbonic anhydrase 1.

X-ray absorption spectroscopy at the Zn K-edge indicates that the active site of the marine diatom Thalassiosira weissflogii carbonic anhydrase is strikingly similar to that of mammalian alpha-carbonic anhydrase enzymes. The zinc has three histidine ligands and a single water at 1.98 A. This is quite different from the beta-carbonic anhydrases of higher plants in which zinc is coordinated by two cysteine thiolates, one histidine, and a water molecule. The diatom carbonic anhydrase shows no significant sequence similarity with other carbonic anhydrases and may represent an example of convergent evolution at the molecular level.

Animals↗
PubMed1992

Comparison of cobalamin-independent and cobalamin-dependent methionine synthases from Escherichia coli: two solutions to the same chemical problem.

In Escherichia coli, two enzymes catalyze the synthesis of methionine from homocysteine using methyltetrahydrofolate as the donor of the required methyl group: cobalamin-dependent and cobalamin-independent methionine synthases. Comparison of the mechanisms of these two enzymes offers the opportunity to examine two different solutions to the same chemical problem. We initiated the research described here to determine whether the two enzymes were evolutionarily related by comparing the deduced amino acid sequences of the two proteins. We have determined the nucleotide sequence for the metE gene, encoding the cobalamin-independent methionine synthase. Our results reveal an absence of similarity between the deduced amino acid sequences of the cobalamin-dependent and cobalamin-independent proteins and suggest that the two have arisen by convergent evolution. We have developed a rapid one-step purification of the recombinant cobalamin-independent methionine synthase (MetE) that yields homogeneous protein in high yield for mechanistic and structural studies. In the course of these studies, we identified a highly reactive thiol in MetE that is alkylated by chloromethyl ketones and by iodoacetamide. We demonstrated that alkylation of this residue, shown to be cysteine 726, results in complete loss of activity. While we are unable to deduce the role of cysteine 726 in catalysis at this time, the identification of this reactive residue suggests the possibility that this thiol functions as an intermediate methyl acceptor in catalysis, analogous to the role of cobalamin in the reaction catalyzed by the cobalamin-dependent enzyme.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
PubMed1991

Structural and evolutionary relationships between retroviral and eucaryotic aspartic proteinases.

Three-dimensional crystal structures of the homologous retroviral proteinases from Rous sarcoma virus (RSV PR) and from human immunodeficiency virus (HIV-1 PR) are to a large extent similar and bear close resemblance to the six known structures of the bilobal fungal and mammalian aspartic proteinases. Systematic three-dimensional structural superpositions were carried out between the retroviral and the eucaryotic aspartic proteinases. Both retroviral enzymes were found to be similarly related to their fungal and mammalian counterparts. The most strongly conserved parts correspond to those regions in the N- and C-domains of the eucaryotic enzymes that are related by the interdomain dyad and consist of a combination of secondary structural elements that form the psi loop-alpha helix motif at the active sites of the aspartic proteinases. The retroviral proteinase monomer exhibits nearly the same degree of structural equivalence to the N- and C-domains of the eucaryotic enzymes. In light of the deduced structural relationships between HIV-1 PR and RSV PR, sequence alignments were performed for a number of retroviral proteinases from different subfamilies. There are three highly conserved amino acid sequence stretches, of which two belong to the psi loop-alpha helix motif, that bear moderate sequence similarity with the eucaryotic enzymes. The third conserved sequence stretch among the retroviral proteinases belongs to the flap and bears no resemblance to the flap sequences in the eucaryotic enzymes. The interdomain antiparallel beta sheet in the cellular enzymes differs from the intersubunit beta sheet in the number, arrangement, and directionality of strands, suggesting the possibility of convergent evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2002

Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta- and gamma-class.

Catalysis of the dehydration of HCO(3)(-) by carbonic anhydrase requires proton transfer from solution to the zinc-bound hydroxide. Carbonic anhydrases in each of the alpha, beta, and gamma classes, examples of convergent evolution, appear to have a side chain extending into the active site cavity that acts as a proton shuttle to facilitate this proton transfer, with His 64 being the most prominent example in the alpha class. We have investigated chemical rescue of mutants in two of these classes in which a proton shuttle has been replaced with a residue that does not transfer protons: H216N carbonic anhydrase from Arabidopsis thaliana (beta class) and E84A carbonic anhydrase from the archeon Methanosarcina thermophila (gamma class). A series of structurally homologous imidazole and pyridine buffers were used as proton acceptors in the activation of CO(2) hydration at steady state and as proton donors of the exchange of (18)O between CO(2) and water at chemical equilibrium. Free energy plots of the rate constants for this intermolecular proton transfer as a function of the difference in pK(a) of donor and acceptor showed extensive curvature, indicating a small intrinsic kinetic barrier for the proton transfers. Application of Marcus rate theory allowed quantitative estimates of the intrinsic kinetic barrier which were near 0.3 kcal/mol with work functions in the range of 7-11 kcal/mol for mutants in the beta and gamma class, similar to results obtained for mutants of carbonic anhydrase in the alpha class. The low values of the intrinsic kinetic barrier for all three classes of carbonic anhydrase reflect proton transfer processes that are consistent with a model of very rapid proton transfer through a flexible matrix of hydrogen-bonded solvent structures sequestered within the active sites of the carbonic anhydrases.

Alanine↗
PubMed2005

Identification and visualization of the dimerization initiation site of the prototype lentivirus, maedi visna virus: a potential GACG tetraloop displays structural homology with the alpha- and gamma-retroviruses.

Dimerization of retroviral genomic RNA is essential for efficient viral replication and is mediated by structural interactions between identical RNA motifs in the viral leader region. We have visualized, by electron microscopy, RNA dimers formed from the leader region of the prototype lentivirus, maedi visna virus. Characterization by in vitro assays of the domains responsible for this interaction has identified a 20 nucleotide sequence that functions as the core dimerization initiation site. This region is predicted to form a GACG tetraloop and therefore differs significantly from the kissing loop palindromes utilized to initiate dimerization in primate lentiviruses. The motif is strongly conserved across the ovine and caprine lentiviruses, implying a critical functional role. Furthermore, the proposed GACG tetraloop exhibits marked structural homology with similar structural motifs present in the leader regions of the alpha- and gamma-retroviruses, and the maedi visna virus dimer linkage region is capable of forming heterodimeric species with the Moloney murine leukemia virus Psi domain. This may be indicative of commonality of origin of the two viruses or convergent evolution.

Animals↗
PubMed2000

Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.

Plant cell wall hydrolases generally have a modular structure consisting of a catalytic domain linked to one or more noncatalytic carbohydrate-binding modules (CBMs), whose common function is to attach the enzyme to the polymeric substrate. Xylanase A from Pseudomonas fluorescens subsp. cellulosa (Pf Xyn10A) consists of a family 10 catalytic domain, an N-terminal family IIa cellulose-binding module, and an internal family 10 cellulose-binding module. The structure of the 45-residue family 10 CBM has been determined in solution using NMR. It consists of two antiparallel beta-sheets, one with two strands and one with three, with a short alpha-helix across one face of the three-stranded sheet. There is a high density of aromatic residues on one side of the protein, including three aromatic residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical polysaccharide-binding arrangement. The fold is closely similar to that of the oligonucleotide/oligosaccharide-binding (OB) fold, but appears to have arisen by convergent evolution, because there is no sequence similarity, and the presumed binding sites are on different faces.

Amino Acid Sequence↗
PubMed2002

How proteins bind carbohydrates: lessons from legume lectins.

The pioneering studies of Irvin Liener on soybean agglutinin (SBA) in the early 1950s served as the starting point of our involvement in lectin research during the past four decades. Initially we characterized SBA extensively as a glycoprotein and showed that its covalently linked glycan is an oligomannoside commonly present in animal glycoproteins. We have also introduced the use of the lectin to the study of normal and malignant cells and to the purging of bone marrow for transplantation. Our recent work focuses on the combining site of Erythrina corallodendron lectin, closely related to SBA. In this legume lectin, as in essentially all other members of the same protein family, irrespective of their sugar specificity, interactions with a constellation of three invariant residues (aspartic acid, asparagine, and an aromatic residue) are essential for ligand binding. Lectins from other families, whether of plants or animals, also combine with carbohydrates by H-bonds and hydrophobic interactions, but the amino acids involved may differ even if the specificity of the lectins is the same. Therefore, nature finds diverse solutions for the design of binding sites for structurally similar ligands, such as mono- or oligosaccharides. This diversity strongly suggests that lectins are products of convergent evolution.

Binding Sites↗
PubMed2000

Multiple-conformation and protonation-state representation in 4D-QSAR: the neurokinin-1 receptor system.

Using a 4D-QSAR approach (software Quasar) allowing for multiple-conformation, orientation, and protonation-state ligand representation as well as for the simulation of local induced-fit phenomena, we have validated a family of receptor surrogates for the neurokinin-1 (NK-1) receptor system. The evolution was based on a population of 500 receptor models and simulated during 40 000 crossover steps, corresponding to 80 generations. It yielded a cross-validated r(2) of 0.887 for the 50 ligands of the training set (represented by a total of 218 conformers and protomers) and a predictive r(2) of 0.834 for the 15 ligands of the test set (70 conformers and protomers). A series of five "scramble tests" (with an average predictive r(2) of -0.438) demonstrates the sensitivity of the surrogate toward the biological data, for which it should establish a QSAR. On the basis of this model, the activities of 12 new compounds - four of which have been synthesized and tested in the meantime - are predicted. For most of the NK-1 antagonists, the genetic algorithm selected a single entity - out of the up to 12 conformers or protomers - to preferably bind to the receptor surrogate. Moreover, the evolution converged at an identical protonation scheme for all NK-1 antagonists. This indicates that 4D-QSAR techniques may, indeed, reduce the bias associated with the choice of the bioactive conformation as each ligand molecule can be represented by an ensemble of conformations, orientations, and protonation states.

Combinatorial Chemistry Techniques↗
PubMed2002

5D-QSAR: the key for simulating induced fit?

In this journal we recently reported the development and the validation of a four-dimensional (4D)-QSAR (quantitative structure-activity relationships) concept, allowing for multiple conformation, orientation, and protonation state representation of ligand molecules. While this approach significantly reduces the bias with selecting a bioactive conformer, orientation, or protonation state, it still requires a "sophisticated guess" about manifestation and magnitude of the associated local induced fit-the adaptation of the receptor binding pocket to the individual ligand topology. We have therefore extended our concept (software Quasar) by an additional degree of freedom--the fifth dimension--allowing for a multiple representation of the topology of the quasi-atomistic receptor surrogate. While this entity may be generated using up to six different induced-fit protocols, we demonstrate that the simulated evolution converges to a single model and that 5D-QSAR--due to the fact that model selection may vary throughout the entire simulation--yields less biased results than 4D-QSAR where only a single induced- fit model can be evaluated at a time. Using two bioregulators (the neurokinin-1 receptor and the aryl hydrocarbon receptor), we compare the results obtained with 4D- and 5D-QSAR. The NK-1 receptor system (represented by a total of 65 antagonist molecules) converges at a cross-validated r2 of 0.870 and a predictive r2 of 0.837; the corresponding values for the Ah receptor system (represented by a total of 131 dibenzodioxins, dibenzofurans, biphenyls, and polyaromatic hydrocarbons) are 0.838 and 0.832, respectively. The results indicate that the formal investment of additional computer time is well-returned both in quantitative and in qualitative values: less-biased boundary conditions, healthier (i.e., less inbred) model populations, and more accurate predictions of new compounds.

Ligands↗
PubMed1997

Oxidative metabolism of inorganic sulfur compounds by bacteria.

The history of the elucidation of the microbiology and biochemistry of the oxidation of inorganic sulfur compounds in chemolithotrophic bacteria is briefly reviewed, and the contribution of Martinus Beijerinck to the study of sulfur-oxidizing bacteria highlighted. Recent developments in the biochemistry, enzymology and molecular biology of sulfur oxidation in obligately and facultatively lithotrophic bacteria are summarized, and the existence of at least two major pathways of thiosulfate (sulfur and sulfide) oxidation confirmed. These are identified as the 'Paracoccus sulfur oxidation' (or PSO) pathway and the 'S4intermediate' (or S4I) pathway respectively. The former occurs in organisms such as Paracoccus (Thiobacillus) versutus and P. denitrificans, and possibly in Thiobacillus novellus and Xanthobacter spp. The latter pathway is characteristic of the obligate chemolithotrophs (e.g. Thiobacillus tepidarius, T. neapolitanus, T. ferrooxidans, T. thiooxidans) and facultative species such as T. acidophilus and T. aquaesulis, all of which can produce or oxidize tetrathionate when grown on thiosulfate. The central problem, as yet incompletely resolved in all cases, is the enzymology of the conversion of sulfane-sulfur (as in the outer [S-] atom of thiosulfate [-S-SO3-]), or sulfur itself, to sulfate, and whether sulfite is involved as a free intermediate in this process in all, or only some, cases. The study of inorganic sulfur compound oxidation for energetic purposes in bacteria (i.e. chemolithotrophy and sulfur photolithotrophy) poses challenges for comparative biochemistry. It also provides evidence of convergent evolution among diverse bacterial groups to achieve the end of energy-yielding sulfur compound oxidation (to drive autotrophic growth on carbon dioxide) but using a variety of enzymological systems, which share some common features. Some new data are presented on the oxidation of 35S-thiosulfate, and on the effect of other anions (selenate, molybdate, tungstate, chromate, vanadate) on sulfur compound oxidation, including observations which relate to the roles of polythionates and elemental sulfur as intermediates.

Gram-Negative Aerobic Bacteria↗
PubMed1997

Maize glutathione-dependent formaldehyde dehydrogenase cDNA: a novel plant gene of detoxification.

We have previously shown that intact plants and cultured plant cells can metabolize and detoxify formaldehyde through the action of a glutathione-dependent formaldehyde dehydrogenase (FDH), followed by C-1 metabolism of the initial metabolite (formic acid). The cloning and heterologous expression of a cDNA for the glutathione-dependent formaldehyde dehydrogenase from Zea mays L. is now described. The functional expression of the maize cDNA in Escherichia coli proved that the cloned enzyme catalyses the NAD(+)- and glutathione (GSH)-dependent oxidation of formaldehyde. The deduced amino acid sequence of 41 kDa was on average 65% identical with class III alcohol dehydrogenase from animals and less than 60% identical with conventional plant alcohol dehydrogenases (ADH) utilizing ethanol. Genomic analysis suggested the existence of a single gene for this cDNA. Phylogenetic analysis supports the convergent evolution of ethanol-consuming ADHs in animals and plants from formaldehyde-detoxifying ancestors. The high structural conservation of present-day glutathione-dependent FDH in microorganisms, plants and animals is consistent with a universal importance of these detoxifying enzymes.

Alcohol Dehydrogenase↗
PubMed1997

A member of the immunoglobulin superfamily in bacteriophage T4.

We report a prediction that the highly immunogenic outer capsid (Hoc) protein of the prokaryotic phage T4 contains three tandem immunoglobulin-like domains. Immunoglobulin-like folds have previously been identified in prokaryotic proteins but these share no recognizable sequence similarity with eukaryotic immunoglobulin superfamily (IgSF) folds, and may represent products of convergent evolution. In contrast, the Hoc immunoglobulin-like folds are proposed, based on immunoglobulin-like sequence consensus matches detected by hidden Markov modeling. We propose that the Hoc immunoglobulin-like domains and eukaryotic immunoglobulin-like domains are likely to be related by divergence from a common ancestor.

Amino Acid Sequence↗
PubMed2003

Random amplified polymorphic DNA diversity among surface and subterranean populations of Asellus aquaticus (Crustacea: Isopoda).

The ecological and evolutionary processes leading to isolation and adaptation of cave animals compared to their surface ancestors are not yet unequivocally understood. In this study the genetic relations of four cave and three surface population of the freshwater crustacean Asellus aquaticus in the Karst region of SW Slovenia and NE Italy were assessed using RAPDs as genetic markers. The results suggest that specialized populations from two caves invaded their subterranean habitat independently, and that their morphological similarity is a result of convergent evolution. Another, less specialized cave population seems to originate from a later colonization of a cave system already inhabited by a more specialized population, but the two populations do not interbreed. This series of temporally and spatially independent invasions has generated a diversity hotspot of non-interbreeding populations of a ubiquitous freshwater crustacean, which is uniform over most of its range. Genetic variability estimated by the percentage of polymorphic RAPD fragments was similar (86-91%) in most cave and surface populations. Substantially lower values (as low as 49%) were found in two cave populations affected by heavy pollution. Two a priori groupings of populations, traditional subspecies and hydrologically connected groups, were rejected as not significant by means of nested analysis of molecular variance (AMOVA). On the other hand, groupings revealed by UPGMA clustering displayed a significant component of among-group variance. An analysis of gene flow between populations using estimated migration rates confirmed these findings.

Animals↗
PubMed2001

The genomic context of natural killer receptor extended gene families.

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 alphaR 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.

Animals↗
PubMed1998

Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease.

Human cytomegalovirus (HCMV) protease belongs to a new class of serine proteases, with a unique polypeptide backbone fold. The crystal structure of the protease in complex with a peptidomimetic inhibitor (based on the natural substrates and covering the P4 to P1' positions) has been determined at 2.7 A resolution. The inhibitor is bound in an extended conformation, forming an anti-parallel beta-sheet with the protease. The P3 and P1 side chains are less accessible to solvent, whereas the P4 and P2 side chains are more exposed. The inhibitor binding mode shows significant similarity to those observed for peptidomimetic inhibitors or substrates of other classes of serine proteases (chymotrypsin and subtilisin). HCMV protease therefore represents example of convergent evolution. In addition, large conformational differences relative to the structure of the free enzyme are observed, which may be important for inhibitor binding.

Amino Acid Sequence↗