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At least 505 records · Page 28Linked to original sources
PubMed2001

Gene and genome duplication.

Genomic sequencing projects have revealed the productivity of processes duplicating genes or entire chromosome segments. Substantial proportions of the yeast, Arabidopsis and human gene complements are made up of duplicates. This has prompted much interest in the processes of duplication, functional divergence and loss of genes, has renewed the debate on whether an early vertebrate genome was tetraploid, and has inspired mathematical models and algorithms in computational biology.

Algorithms↗
PubMed2001

Fish gonadotropin and thyrotropin receptors: the evolution of glycoprotein hormone receptors in vertebrates.

We have cloned and characterized, for the first time in fish, two different gonadotropin receptors (GTHR) and a single thyrotropin receptor (TSHR) from amago salmon (Oncorhynchus rhodurus) and Nile tilapia (Oreochromis niloticus). Phylogenetic analyses and intron/exon structure suggest that the two GTHRs in fish are comparable to tetrapod follicle stimulating hormone and luteinizing hormone receptors. Temporal and spatial expression patterns, examined by Northern blot analysis and in situ hybridization, paralleled those seen in mammals and birds. Consequently, genetic and functional divergence of two GTHRs and TSHR probably occurred before the teleost and tetrapod split.

Animals↗
PubMed2000

The divergent role of tumor necrosis factor receptors in infectious diseases.

Tumor necrosis factor (TNF) receptor types 1 and 2 are broadly expressed by most cell types and are activated by binding of either TNF or lymphotoxin-beta. TNF receptor-mediated immune reactions are critically important in the pathogenesis and control of a variety of infections caused by bacteria, viruses, protozoa, and fungi. This review summarizes recent findings on the role of TNF receptors in infectious diseases and discusses the divergent functions of these receptors in immune responses.

Bacterial Infections↗
PubMed2002

Mutator transposons.

Mutator (Mu) element insertion has become the main way of mutating and cloning maize genes, but we are only beginning to understand how this transposon system is regulated. Mu elements are under tight developmental control and are subject to a form of epigenetic regulation that shares some features with the regulation of paramutable maize genes. Mu-like elements (MULEs) are widespread among angiosperms, and multiple diverged functional variants appear to have coexisted in genomes for long periods. In addition to its utility, the means by which this widespread and highly mutagenic system is held in check should help us to address fundamental issues concerning the stability of genomes.

Amino Acid Sequence↗
PubMed1987

Complete cDNA sequence of human complement Cls and close physical linkage of the homologous genes Cls and Clr.

Overlapping molecular clones encoding the complement subcomponent Cls were isolated from a human liver cDNA library. The nucleotide sequence reconstructed from these clones spans about 85% of the length of the liver Cls messenger RNAs, which occur in three distinct size classes around 3 kilobases in length. Comparisons with the sequence of Clr, the other enzymatic subcomponent of Cl, reveal 40% amino acid identity and conservation of all the cysteine residues. Beside the serine protease domain, the following sequence motifs, previously described in Clr, were also found in Cls: (a) two repeats of the type found in the Ba fragment of complement factor B and in several other complement but also noncomplement proteins, (b) a cysteine-rich segment homologous to the repeats of epidermal growth factor precursor, and (c) a duplicated segment found only in Clr and Cls. Differences in each of these structural motifs provide significant clues for the interpretation of the functional divergence of these interacting serine protease zymogens. Hybridizations of Clr and Cls probes to restriction endonuclease fragments of genomic DNA demonstrate close physical linkage of the corresponding genes. The implications of this finding are discussed with respect to the evolution of Clr and Cls after their origin by tandem gene duplication and to the previously observed combined hereditary deficiencies of Clr and Cls.

Amino Acid Sequence↗
PubMed2005

Identification of functional amino acids in the Nramp family by a combination of evolutionary analysis and biophysical studies of metal and proton cotransport in vivo.

The natural resistance-associated macrophage protein (Nramp) family is functionally conserved in bacteria and eukarya; Nramp homologues function as proton-dependent membrane transporters of divalent metals. Sequence analyses indicate that five phylogenetic groups comprise the Nramp family, three bacterial and two eukaryotic, which are distinct from a more distantly related group of microbial sequences (Nramp outgroup). The Nramp family and outgroup share many conserved residues, suggesting they derived from a common ancestor and raising the possibility that the residues invariant in the Nramp family that correspond to residues which are different but also conserved in the outgroup represent candidate sites of functional divergence of the Nramp family. Four Nramp family-specific residues were identified within transmembrane domains 1, 6, and 11, and replaced by the corresponding invariant outgroup residues in the Escherichia coli Nramp ortholog (the proton-dependent manganese transporter, MntH of group A, EcoliA). The resulting mutants (Asp(34)Gly, Asn(37)Thr, His(211)Tyr, and Asn(401)Gly) were tested for both divalent metal uptake and proton transport; quasi-simultaneous analyses of uptake of metals and protons revealed for the first time protons and metals cotransport by a bacterial Nramp homologue. Additional mutations were studied for comparison (Asp(34)Asn, Asn(37)Asp and Asn(37)Val, Asn(401)Thr, His(211)Ala, His(216)Ala, and His(216)Arg). EcoliA activity was impaired after each of the Nramp/outgroup substitutions, as well as after more conservative replacements, showing that the tested sites are all important for metal uptake and metal-dependent H(+) transport. It is proposed that co-occurrence of these four Nramp-specific transmembrane residues may have contributed to the emergence of this family of metal and proton cotransporters.

Amino Acids↗
PubMed2004

Toward the insulin-IGF-I intermediate structures: functional and structural properties of the [TyrB25NMePheB26] insulin mutant.

The origins of differentiation of insulin from insulin-like growth factor I (IGF-I) are still unknown. To address the problem of a structural and biological switch from the mostly metabolic hormonal activity of insulin to the predominant growth factor activities of IGF-I, an insulin analogue with IGF-I-like structural features has been synthesized. Insulin residues Phe(B25) and Tyr(B26) have been swapped with the IGF-I-like Tyr(24) and Phe(25) sequence with a simultaneous methylation of the peptide nitrogen of residue Phe(B26). These modifications were expected to introduce a substantial kink in the main chain, as observed at residue Phe(25) in the IGF-I crystal structure. These alterations should provide insight into the structural origins of insulin-IGF-I structural and functional divergence. The [Tyr(B25)NMePhe(B26)] mutant has been characterized, and its crystal structure has been determined. Surprisingly, all of these changes are well accommodated within an insulin R6 hexamer. Only one molecule of each dimer in the hexamer responds to the structural alterations, the other remaining very similar to wild-type insulin. All alterations, modest in their scale, cumulate in the C-terminal part of the B-chain (residues B23-B30), which moves toward the core of the insulin molecule and is associated with a significant shift of the A1 helix toward the C-terminus of the B-chain. These changes do not produce the expected bend of the main chain, but the fold of the mutant does reflect some structural characteristics of IGF-1, and in addition establishes the CO(A19)-NH(B25) hydrogen bond, which is normally characteristic of T-state insulin.

Animals↗
PubMed2004

Membrane association, electrostatic sequestration, and cytotoxicity of Gly-Leu-rich peptide orthologs with differing functions.

The skins of closely related frog species produce Gly-Leu-rich peptide orthologs that have very similar sequences, hydrophobicities, and amphipathicities but differ markedly in their net charge and membrane-damaging properties. Cationic Gly-Leu-rich peptides are hemolytic and very potent against microorganisms. Peptides with no net charge have only hemolytic activity. We have used ancestral protein reconstruction and peptide analogue design to examine the roles of electrostatic and hydrophobic interactions in the biological activity and mode of action of functionally divergent Gly-Leu-rich peptides. The structure and interaction of the peptides with anionic and zwitterionic model membranes were investigated by circular dichroism with 2-dimyristoyl-sn-glycero-3-phosphatidylcholine or 1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol vesicles and surface plasmon resonance with immobilized bilayers. The results, combined with antimicrobial assays, the kinetics of bacterial killing, and membrane permeabilization assays, reveal that Gly, Val, Thr, and Ile can all be accommodated in an amphipathic alpha helix when the helix is in a membrane environment. Binding to anionic and zwitterionic membranes fitted to a 2-stage interaction model (adsorption to the membrane followed by membrane insertion). The first step is governed by hydrophobic interactions between the nonpolar surface of the peptide helix and the membranes. The strong binding of Gly-Leu-rich cationic peptides to anionic membranes is due to the second binding step and involves short-range Coulombic interactions that prolong the residence time of the membrane-inserted peptide. The data demonstrate that evolution has positively selected charge-altering nucleotide substitutions to generate an orthologous cationic variant of neutral hemolytic peptides that bind to and permeate bacterial cell membranes.

Amino Acid Sequence↗
PubMed2005

Mitochondrial and microsomal ferric b5 cytochromes exhibit divergent conformational plasticity in the context of a common fold.

Native-state hydrogen-deuterium exchange (HDX) monitored by NMR spectroscopy has been used to compare conformational plasticity in ferric rat liver outer mitochondrial membrane cytochrome b5 (rOM b5) and ferric bovine liver microsomal cytochrome b5 (bMc b5). Analysis of the data indicated that rOM b5 is the less conformationally flexible protein on the time scale probed by the HDX experiments. The data also suggest a likely contributor to the much higher kinetic barrier for the release of hemin from OM b5s in comparison to Mc b5s, a characteristic that may be to a large extent the source of their divergent functional properties. Specifically, the data indicate that conformational mobility within helices alpha4 and alpha5, which flank the loop harboring axial ligand His63, is considerably more restricted in rOM b5 than in bMc b5. The lower conformational flexibility of alpha4 and alpha5 in rOM b5 can reasonably be attributed to more extensive hydrophobic packing in that region of the protein, arising from two conserved side chain packing motifs in OM cytochrome b5s [Altuve, A., Wang, L., Benson, D. R., and Rivera, M. (2004) Biochem. Biophys. Res. Commun. 314, 602-609].

Amino Acid Sequence↗
PubMed2006

Structural studies of a potent insect maturation inhibitor bound to the juvenile hormone esterase of Manduca sexta.

Juvenile hormone (JH) is an insect hormone containing an alpha,beta-unsaturated ester consisting of a small alcohol and long, hydrophobic acid. JH degradation is required for proper insect development. One pathway of this degradation is through juvenile hormone esterase (JHE), which cleaves the JH ester bond to produce methanol and JH acid. JHE is a member of the functionally divergent alpha/beta-hydrolase family of enzymes and is a highly efficient enzyme that cleaves JH at very low in vivo concentrations. We present here a 2.7 A crystal structure of JHE from the tobacco hornworm Manduca sexta (MsJHE) in complex with the transition state analogue inhibitor 3-octylthio-1,1,1-trifluoropropan-2-one (OTFP) covalently bound to the active site. This crystal structure, the first JHE structure reported, contains a long, hydrophobic binding pocket with the solvent-inaccessible catalytic triad located at the end. The structure explains many of the interactions observed between JHE and its substrates and inhibitors, such as the preference for small alcohol groups and long hydrophobic backbones. The most potent JHE inhibitors identified to date contain a trifluoromethyl ketone (TFK) moiety and have a sulfur atom beta to the ketone. In this study, sulfur-aromatic interactions were observed between the sulfur atom of OTFP and a conserved aromatic residue in the crystal structure. Mutational analysis supported the hypothesis that these interactions contribute to the potency of sulfur-containing TFK inhibitors. Together, these results clarify the binding mechanism of JHE inhibitors and provide useful observations for the development of additional enzyme inhibitors for a variety of enzymes.

Acetone↗
PubMed1996

Chemical synthesis of a Zwitterhormon, insulaxin, and of a relaxin-like bombyxin derivative.

The structural motif of insulin and relaxin is frequently seen in molecules of divergent functions and origins. The insect developmental factor bombyxin, the relaxin-like factor from Leydig cells, and the insulin-like factor 4 (INSL4) all are made of two disulfide-linked chains and have one disulfide bond within the A-chain. The polyclonal antibody R6, which was raised against porcine relaxin, reacts with a wide variety of naturally occurring relaxins from primates, marine and terrestrial mammals, and elasmobranchs but does not recognize insulin. The antibody binds mainly to the arginines that occur in the N, N+4 positions in the B-chains of all relaxins which also constitute the receptor-binding site. The receptor-binding haptens were incorporated by total synthesis into human despentapeptide insulin and bombyxin II, a developmental factor from the silk moth Bombyx mori. In the process the insect factor became a perfect antigen for the anti-relaxin antibody, whereas the human insulin was transformed into a bona fide relaxin. The conversion was affected by changing four critical residues so that the insulin activity was retained to the extent of 10% of the original level. This, to the best of our knowledge, is the first designer protein to incorporate two unrelated biological functions in one primary sequence, and we are therefore proposing that, analogous to zwitterion, the generic name "Zwitterhormon" (German spelling) be used for this type of construct.

Amino Acid Sequence↗
PubMed1999

Interactions of endothelin receptor subtypes A and B with Gi, Go, and Gq in reconstituted phospholipid vesicles.

To understand the biochemical basis for the functional divergence of the human endothelin receptor subtypes A (ETAR) and B (ETBR), they were expressed, purified from insect Sf9 cells, and reconstituted into phospholipid vesicles with the Go, Gq, and Gi proteins. For each G protein, a unique pattern of reactivity was observed with the different receptor subtypes. Both ETAR and ETBR activated Go to a similar maximal extent, and both subtypes activated Gq with similar EC50 values; however, the ETAR displayed a 2-3-fold higher maximal extent of activation. In contrast, both subtypes activated Gi to a similar maximal extent, but the ETAR displayed a 4-fold higher EC50 value as compared to the ETBR. To test whether these coupling specificities are influenced by C-terminal palmitoylation of the receptor, we mutated a cluster of cysteine residues near the end of the seventh transmembrane helix in both receptors. While the cysteine mutations in the ETBR resulted in a partially palmitoylated receptor, the replacement of these cysteine residues in the ETAR yielded a mostly palmitoyl-deficient receptor and had no effect on Go activation, but caused a reduction in the extents of Gi and Gq stimulation. Together, these studies provide important insights into the specificity of G protein coupling in the endothelin receptors. The ability to discriminate between the different G proteins under various physiological conditions may be a key element in the selection of distinct signal transduction pathways by the two receptor subtypes.

Amino Acid Sequence↗
PubMed1999

The sen1(+) gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase.

Two polynucleotide-dependent ATPases, 95 and 181 kDa in size, have been purified to near homogeneity from cell-free extracts of Schizosaccharomyces pombe. Despite their size differences, their biochemical properties were strikingly similar. Both enzymes were capable of unwinding RNA and DNA duplexes in keeping with their ability to hydrolyze ATP in the presence of either ribo- or deoxyribopolynucleotide. In addition, they were capable of unwinding DNA/RNA or RNA/DNA hybrid duplexes and translocated in the 5' to 3' direction. These results strongly indicate that they are closely related to each other. Determination of the partial amino acid sequence of the 95-kDa enzyme revealed that it is encoded by the sen1(+)() gene, an S. pombe homologue of yeast SEN1, a protein essential for the processing of small nucleolar RNA, transfer RNA, and ribosomal RNA. The molecular weight of the S. pombe Sen1 protein (SpSen1p) predicted from the sen1(+)() open reading frame was 192.5 kDa, suggesting that the 181-kDa enzyme is likely to be a full-length protein, whereas the 95-kDa polypeptide has arisen by proteolysis. In accord with this possibility, polyclonal antibodies specific to the C-terminal region of sen1(+)() cross-reacted with both 95- and 181-kDa polypeptides. We discuss the biochemical activities associated with SpSen1p and their relevance to the apparently divergent functions ascribed to the yeast Sen1 protein in RNA metabolism.

Adenosine Triphosphatases↗
PubMed2006

Enzymatic formation of quinolone alkaloids by a plant type III polyketide synthase.

[Structure: see text] Benzalacetone synthase from Rheum palmatum efficiently catalyzed condensation of N-methylanthraniloyl-CoA (or anthraniloyl-CoA) with malonyl-CoA (or methylmalonyl-CoA) to produce 4-hydroxy-2(1H)-quinolones, a novel alkaloidal scaffold produced by a type III polyketide synthase (PKS). Manipulation of the functionally divergent type III PKSs by a nonphysiological substrate thus provides an efficient method for production of pharmaceutically important quinolone alkaloids.

Alkaloids↗
PubMed2004

Caspase-9 regulation: an update.

The complex sequence of events leading to apoptotic cell death is governed by an elaborate regulatory scheme involving the actions of both initiator and executioner proteases. Among the most intensively studied of the initiator caspases is caspase-9, an essential throughput element in the so-called intrinsic or mitochondrially gated pathway of apoptosis. Previous reviews have described the proteolytic processing and activation of this protease in much detail; here we provide an update on caspase-9 regulation. A comprehensive description of the intra- and intermolecular events involved in modulating protein expression and activity are presented. Particular emphasis is placed on the role alternative splicing plays in the expression of functionally divergent protein isoforms, as well as, the participation of specific post-translational events in regulating caspase-9 activity. Such discrete modulation in reported activity characterizes, not only the pivotal role of this protease in the final commitment process itself, but also emphasizes the more general interplay that exists between mutually opposing cytotoxic and cytoprotective influences in maintaining cellular homeostasis.

Alternative Splicing↗
PubMed2004

Cytosolic, mitochondrial thioredoxins and thioredoxin reductases in Arabidopsis thaliana.

Thioredoxins, by reducing disulfide bridges are one of the main participants that regulate cellular redox balance. In plants, the thioredoxin system is particularly complex. The most well-known thioredoxins are the chloroplastic ones, that participate in the regulation of enzymatic activities during the transition between light and dark phases. The mitochondrial system composed of NADPH-dependent thioredoxin reductase and type o thioredoxin has only recently been described. The type h thioredoxin group is better known. Yeast complementation experiments demonstrated that Arabidopsis thaliana thioredoxins h have divergent functions, at least in Saccharomyces cerevisiae. They have diverse affinities for different target proteins, most probably because of structural differences. However, plant thioredoxin h functions still have to be defined.

Journal Article↗
PubMed1992

Adult age differences in the rate of learning serial patterns: evidence from direct and indirect tests.

Subjects performed a serial reaction time task (adopted from Nissen & Bullemer, 1987) that contained a repeating pattern of spatial locations. In Experiment 1, following 20 repetitions of a 10- or 16-element pattern, reaction time was equally disrupted for both younger and older people when the sequence became random. In Experiment 2, the response times for subjects encountering the 10-element pattern were compared with those of subjects encountering a random sequence. These response time functions diverged at the same point in training for the 2 age groups. Thus, on this indirect measure of response time facilitation, both experiments revealed age similarity in the rate of pattern learning. In contrast, on a subsequent direct test of pattern learning that required prediction, the younger people earned a higher percentage correct score than the older in both experiments. Age-related dissociations between direct and indirect measures of learning and comparisons with memory-impaired populations are discussed.

Adolescent↗
PubMed1989

Reconstruction of an enzyme by domain substitution effectively switches substrate specificity.

The polar domains of the two transcarbamoylases, aspartate transcarbamoylase (ATCase) and ornithine transcarbamoylase, (OTCase) from Escherichia coli bind the common substrate carbamoyl phosphate and share extensive amino-acid sequence homology. The equatorial domains of the two enzymes differ in their substrate specificity (ATCase binds aspartate, OTCase binds ornithine) and have decreased sequence identity. While addressing the conservation of specific protein interactions during the evolution of these enzymes, we were able to switch one of their amino-acid-specific equatorial domains to produce a viable chimaeric enzyme. This was achieved by the in vitro fusion of DNA encoding the polar domain of OTCase to DNA encoding the equatorial domain of ATCase. The resulting gene fusion successfully transformed an argI-pyrB deletion strain of E. coli to pyrimidine prototrophy, giving rise to Pyr+ transformants that expressed ATCase but not OTCase activity. The formation of this active chimaeric enzyme shows that by exchanging protein domains between two functionally divergent enzymes we have achieved a switching in substrate specificity.

Aspartate Carbamoyltransferase↗