Secretory ribonucleases in the primitive ruminant chevrotain (Tragulus javanicus).

Phylogenetic analyses of secretory ribonucleases or RNases 1 have shown that gene duplication events, giving rise to three paralogous genes (pancreatic, seminal and brain RNase), occurred during the evolution of ancestral ruminants. A higher number of paralogous sequences are present in chevrotain (Tragulus javanicus), the earliest diverged taxon within the ruminants. Two pancreatic RNase sequences were identified, one encoding the pancreatic enzyme, the other encoding a pseudogene. The identity of the pancreatic enzyme was confirmed by isolation of the protein and N-terminal sequence analysis. It is the most acidic pancreatic ribonuclease identified so far. Formation of the mature enzyme requires cleavage by signal peptidase of a peptide bond between two glutamic acid residues. The seminal-type RNase gene shows features of a pseudogene, like orthologous genes in other ruminants investigated with the exception of the bovine species. The brain-type RNase gene of chevrotain is expressed in brain tissue. A hybrid gene with a pancreatic-type N-terminal and a brain-type C-terminal sequence has been identified but nothing is known about its expression. Phylogenetic analysis of RNase 1 sequences of six ruminant, three other artiodactyl and two whale species support previous findings that two gene duplications occurred in a ruminant ancestor. Three distinct groups of pancreatic, seminal-type and brain-type RNases have been identified and within each group the chevrotain sequence it the first to diverge. In taxa with duplications of the RNase gene (ruminants and camels) the gene evolved at twice as fast than in taxa in which only one gene could be demonstrated; in ruminants there was an approximately fourfold increase directly after the duplications and then a slowing in evolutionary rate.

Ruminant brain ribonucleases: expression and evolution.

Molecular evolutionary analyses of mammalian ribonucleases have shown that gene duplication events giving rise to three paralogous genes occurred in ruminant ancestors. One of these genes encodes a ribonuclease identified in bovine brain. A peculiar feature of this enzyme and orthologous sequences in other ruminants are C-terminal extensions consisting of 17-27 amino acid residues. Evidence was obtained by Western blot analysis for the presence of brain-type ribonucleases in brain tissue not only of ox, but also of sheep, roe deer and chevrotain (Tragulus javanicus), a member of the earliest diverged taxon of the ruminants. The C-terminal extension of brain-type ribonuclease from giraffe deviates much in sequence from orthologues in other ruminants, due to a change of reading frame. However, the gene encodes a functional enzyme, which could be expressed in heterologous systems. The messenger RNA of bovine brain ribonuclease is not only expressed at a high level in brain tissue but also in lactating mammary gland. The enzyme was isolated and identified from this latter tissue, but was not present in bovine milk, although pancreatic ribonucleases A and B could be isolated from both sources. This suggests different ways of secretion of the two enzyme types, possibly related to structural differences. The sequence of the brain-type RNase from chevrotain suggests that the C-terminal extensions of ruminant brain-type ribonucleases originate from deletions in the ancestral DNA (including a region with stop codons), followed by insertion of a 5-8-fold repeated hexanucleotide sequence, coding for a proline-rich polypeptide.

Seminal-type ribonuclease genes in ruminants, sequence conservation without protein expression?

Bovine seminal ribonuclease (BS-RNase) is an interesting enzyme both for functional and structural reasons. The enzyme is the product of a gene duplication that occurred in an ancestral ruminant. It is possible to demonstrate the presence of seminal-type genes in all other investigated ruminant species, but they are not expressed and show features of pseudogenes. In this paper we report the determination of two pancreatic and one seminal-type ribonuclease gene sequences of swamp-type water buffalo (Bubalus bubalis). The two pancreatic sequences encode proteins with identical amino acid sequences as previously determined for the enzymes isolated from swamp-type and river-type water buffalo, respectively. The seminal-type sequence has no pseudogene features and codes for an enzyme with no unusual features compared with the active bovine enzyme, except for the replacement of one of the cysteines which takes part in the two intersubunit disulfide bridges. However, Western blotting demonstrates the presence of only small amounts of the pancreatic enzymes in water buffalo semen, suggesting that also in this species the seminal-type sequence is not expressed. But it is still possible that the gene is expressed somewhere else in the body or during development. Reconstruction of seminal-type ribonuclease sequences in ancestors of Bovinae and Bovidae indicates no serious abnormalities in the encoded proteins and leads us to the hypothesis that the ruminant seminal-type ribonuclease gene has not come to expression during most of its evolutionary history, but did not exhibit a high evolutionary rate that is generally observed in pseudogenes.

Isolation of protease-free alcohol dehydrogenase (ADH) from Drosophila simulans and several homozygous and heterozygous Drosophila melanogaster variants.

The enzyme alcohol dehydrogenase (ADH) from several naturally occurring ADH variants of Drosophila melanogaster and Drosophila simulans was isolated. Affinity chromatography with the ligand Cibacron Blue and elution with NAD+ showed similar behavior for D. melanogaster ADH-FF, ADH-71k, and D. simulans ADH. Introduction of a second Cibacron Blue affinity chromatography step, with gradient elution with NAD+, resulted in pure and stable enzymes. D. melanogaster ADH-SS cannot be eluted from the affinity chromatography column at a high concentration of NAD+ and required a pH gradient for its purification, preceded by a wash step with a high concentration of NAD+. Hybrid Drosophila melanogaster alcohol dehydrogenase FS has been isolated from heterozygous flies, using affinity chromatography with first elution at a high concentration NAD+, directly followed by affinity chromatography elution with a pH gradient. Incubation of equal amounts of pure homodimers of Drosophila melanogaster ADH-FF and ADH-SS, in the presence of 3 M urea at pH 8.6, for 30 min at room temperature, followed by reassociation yielded active Drosophila melanogaster ADH-FS heterodimers. No proteolytic degradation was found after incubation of purified enzyme preparations in the absence or presence of SDS, except for some degradation of ADH-SS after very long incubation times. The thermostabilities of D. melanogaster ADH-71k and ADH-SS were almost identical and were higher than those of D. melanogaster ADH-FF and D. simulans ADH. The thermostability of D. melanogaster ADH-FS was lower than those of D. melanogaster ADH-FF and ADH-SS. D. melanogaster ADH-FF and ADH-71k have identical inhibition constants with the ligand Cibacron Blue at pH 8.6, which are two times higher at pH 9.5. The Ki values for D. simulans ADH are three times lower at both pH values. D. melanogaster ADH-SS and ADH-FS have similar Ki values, which are lower than those for D. melanogaster ADH-FF at pH 8.6. But at pH 9.5 the Ki value for ADH-FS is the same as at pH 8.6, while that of ADH-SS is seven times higher. Kinetic parameters of Drosophila melanogaster ADH-FF, ADH-SS, and ADH-71k and Drosophila simulans ADH, at pH 8.6 and 9.5, showed little or no variation in K(m)eth values. The K(m)NAD values measured at pH 9.5 for Drosophila alcohol dehydrogenases are all lower than those measured at pH 8.6. The rate constants (kcat) determined for all four Drosophila alcohol dehydrogenases are higher at pH 9.5 than at pH 8.6. D. melanogaster ADH-FS showed nonlinear kinetics.

Primary structures of two ribonucleases from ginseng calluses. New members of the PR-10 family of intracellular pathogenesis-related plant proteins.

The amino acid sequences of two ribonucleases from a callus cell culture of Panax ginseng were determined. The two sequences differ at 26% of the amino acid positions. Homology was found with a large family of intracellular pathogenesis-related proteins, food allergens and tree pollen allergens from both dicotyledonous and monocotyledonous plant species. There is about 30% sequence difference with proteins from species belonging to the same plant order (Apiales: parsley and celery), 60% with those from four other dicotyledonous plant orders and about 70% from that of the monocotyledonous asparagus. More thorough evolutionary analyses of sequences lead to the conclusion that the general biological function of members of this protein family may be closely related to the ability to cleave intracellular RNA and that they have an important role in cell metabolism. As the three-dimensional structure of one of the members of this protein family has been determined recently [Gajhede et al., Nature Struct Biol 3 (1996) 1040-1045], it may be possible to assign active-site residues in the enzyme molecule and make hypotheses about its mode of action. Structural features in addition to the cellular site of biosynthesis indicate that this family of ribonucleases is very different from previously investigated ones.

Dimerization of an antigenic peptide leads to strong interaction with its antibody.

A sequential epitope reacting with a monoclonal antibody against Panulirus interruptus hemocyanin was localized in the C-terminal CNBr peptide. As the antibody reacted with about equal affinity with different subunits of this and with hemocyanin from another spiny lobster, Palinurus vulgaris, the epitope was assigned to a conserved sequence region. The CNBr peptide, which was linked to another peptide via a disulfide bridge, was reduced and reoxidized. As a result, not the heterodimer but only the two disulfide-linked homodimers were formed. The dimeric C-terminal peptide had a much higher affinity for the monoclonal antibody than the monomeric peptide. This may be explained by the presence of two independent mobile interaction sites in each of the two reacting molecules.

Primary structure of hemocyanin from Palinurus vulgaris.

The primary structure of hemocyanin from the spiny lobster Palinurus vulgaris was determined using a mixture of at least four slightly different subunits. Heterogeneities were observed in 32 (5%) of the positions. The amino acid sequence differs at about 20% of the positions from that of subunit a of Panulirus interruptus hemocyanin.

Primary structure of hemocyanin subunit c from Panulirus interruptus.

The amino acid sequence of the hemocyanin subunit c from the spiny lobster, Panulirus interruptus, has been determined. The elucidation was mainly based on three digests, with CNBr, trypsin and endoproteinase Glu-C, respectively. Additional evidence was obtained by sequencing of peptides from an endoproteinase Lys-C digest. Subunit c is a polypeptide with 661 amino acid residues and with a carbohydrate group attached to residue 476 in the third domain. No heterogeneity was observed. The degree of identity with subunit a is 59%. Some differences with subunit a are an N-terminal extension of six residues, a one-residue C-terminal extension, and a three-residue deletion. Furthermore, carbohydrate attachment is in a different position, as are most half-cystine residues. Limited trypsinolysis resulted in cleavage at the same site as in subunits a and b.

The primary structure of hevamine, an enzyme with lysozyme/chitinase activity from Hevea brasiliensis latex.

The primary structure of hevamine, an enzyme with lysozyme/chitinase activity from Hevea brasiliensis latex, has been determined predominantly with conventional non-automatic methods. The positions of three disulfide bridges have been determined. The sequence has about 60% identity with that of a chitinase from cucumber and 95% with the N-terminal sequence of the lysozyme/chitinase of Parthenocissus quinquefolia. The half-cystine residues in hevein and cucumber chitinase are located at identical positions. Hevamine is a basic protein from the lutoids (vacuoles) of rubber latex and may have a role in plugging the latex vessels and cessation of latex flow. The differences in cellular location, charge properties and sequence between hevamine and cucumber chitinase are similar to those between class I and class II chitinases from tobacco and other plant species.

Ribonuclease in different chromosomal species of the mole rat, superspecies Spalax ehrenbergi: concentration in the pancreas and primary structure.

Ribonucleases are found in considerable quantities in the pancreas of a number of mammalian taxa and a few reptiles. The ribonuclease content varies greatly in different species. Large quantities are found in ruminants and species that have a ruminant-like digestion and in a number of species with coecal digestion. This is a response to the necessity of digesting large amounts of RNA derived from the microflora of the stomach of ruminants or species with ruminant-like digestion or of the coecum of species with coecal digestion. The amino acid sequence of pancreatic ribonuclease from the chromosomal species 2n = 60 of the mole rat, superspecies Spalax Ehrenbergi was determined. From the comparison of the sequence with those of other mammalian species we found that Spalax diverged from the myomorph rodent branch before the divergence of the Muridae (mouse, rat) from the Cricetidae (hamster, muskrat). Spalax ribonuclease shares several amino acid residues with other myomorph rodent species. These are not or only rarely observed outside this rodent suborder. Although the ribonuclease content varies greatly in different mammalian species, the variation in content between individuals within a species is small. Spalax is an exception to this with ribonuclease contents varying over more than an order of magnitude in different individuals. Ribonucleases isolated from the chromosomal species 2n = 52, 2n = 58 and 2n = 60 have identical elution positions on reversed-phase HPLC. The enzyme from the 2n = 54 species, however, elutes at a slightly earlier elution position. No amino acid sequence differences have been found hitherto between the ribonucleases of the four chromosomal species of Spalax ehrenbergi occurring in Israel. However, due to lack of material we were unable to determine more than about 20% of the sequence of the enzyme from the 2n = 54 species, which is the oldest offshoot.

Panulirus interruptus hemocyanin. The amino acid sequence of subunit b and anomalous behaviour of subunits a and b on polyacrylamide gel electrophoresis in the presence of SDS.

The primary structure of subunit b of Panulirus interruptus hemocyanin has been derived from two digests (trypsin and CNBr) and, in some cases, with aid from the similarity with the sequence of subunit a. Differences between the amidation states of Asx and Glx residues in subunit b relative to a were investigated more thoroughly. When compared to the sequence of subunit a, 18 differences (2.7%) were found and certain heterogeneities, indicating the presence of a minor subunit b', were observed. Several differences in properties between subunits a and b, including their anomalous behaviour on SDS/polyacrylamide gel electrophoresis, could be explained by amino acid replacements.

Chemical modification of tyrosine-38 in p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens by 5'-p-fluorosulfonylbenzoyladenosine: a probe for the elucidation of the NADPH binding site? Involvement in catalysis, assignment in sequence and fitting to the tertiary structure.

p-Hydroxybenzoate hydroxylase from Pseudomonas fluorescens was covalently modified by the nucleotide analog 5'-(p-fluorosulfonylbenzoyl)-adenosine in the presence of 20% dimethylsulfoxide. The inactivation reaction is pH-dependent and does not obey pseudo-first-order kinetics, due to spontaneous hydrolysis of the reagent. The kinetic data further indicate that a weak, reversible enzyme-inhibitor complex is an intermediate in the inactivation reaction and that only one amino acid residue is responsible for the loss of activity. The inactivation is strongly inhibited by NADPH and 2',5'ADP. Steady-state kinetics and 2',5'ADP bioaffinity chromatography of the modified enzyme suggest that the essential residue is not directly involved in NADPH binding. Sequence studies show that Tyr-38 is the main residue protected from modification in the presence of NADPH. From crystallographic studies it is known that the hydroxyl group of Tyr-38 is 1.84 nm away from the active site. Model-building studies using computer graphics show that this distance can be accommodated when FSO2BzAdo binds in an extended conformation with the sulfonylbenzoyl portion in an orientation different from the nicotin-amide ring of NADPH.

Primary and tertiary structures of the first domain of Panulirus interruptus hemocyanin and comparison of arthropod hemocyanins.

The amino acid sequence of the first domain (positions 1-175) of Panulirus interruptus hemocyanin subunit a has been determined. The sequence of residues 1-158 (18-kDa fragment obtained by limited proteolysis) was derived from peptides obtained by digestion of this fragment with CNBr and trypsin and by subdigestion of these peptides with other enzymes. The peptides were sequences automatically or manually. The amino acid sequence has been fitted into the electron-density map at 0.32-nm resolution. The residues of domain 1 are folded into a large, mainly helical, globular part, containing one disulfide bridge, and a smaller part near the molecular twofold axis. The latter part consists of an alpha helix and a beta strand which contains a covalently attached carbohydrate moiety. The sites susceptible to limited proteolytic cleavage of the subunit are discussed. Comparison of the N-terminal sequence with those of other arthropod hemocyanins revealed, besides an N-terminal extension of five residues, the presence of a 21-residue loop (positions 22-42) in the crustacean sequences. This loop contains helix 1.2, a less defined region in the electron-density map. It is absent in chelicerate sequences. Strong evidence is presented that: (a) the structure of the first 21 residues (including helix 1.1) is the same in all arthropod hemocyanins with known amino acid sequence; (b) a stretch containing about 15 residues (including part of helix 1.3) following the 21-residue loop has a different structure in crustaceans and chelicerates; (c) the rest of domain 1 has the same structure again. It is shown that all conserved residues are in the contact region with the other two domains.

Chemical modification of tyrosine residues in p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens: assignment in sequence and catalytic involvement.

p-Hydroxybenzoate hydroxylase was modified by diethyl pyrocarbonate at pH values greater than 7 and by p-diazobenzoate. Modification of the enzyme by diethyl pyrocarbonate abolishes the affinity of the enzyme for the substrate p-hydroxybenzoate. Modification by p-diazobenzoate has the same effect on the enzyme. The enzyme is protected against these modifications by the effector p-fluorobenzoate. The data indicate that the modification of one tyrosine residue in the active center of the enzyme is responsible for the loss of enzyme activity. This tyrosine residue has been identified by sequence studies using radioactively labeled p-diazobenzoate and was found to be most probably Tyr-222. Diethyl pyrocarbonate reacts with a tyrosine residue in the active center other than Tyr-222; the former could not be identified. Sequence studies further showed that Cys-211 is also partially modified by p-diazobenzoate. In addition, the sequence of residues 343-345 was found to be Ser-Trp-Trp instead of the tentative assignment Ser-Tyr-Trp made earlier. The results are briefly discussed on the basis of the existing three-dimensional model of the enzyme.

Chemical modification of sulfhydryl groups in p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens. Involvement in catalysis and assignment in the sequence.

The cysteine residues in p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens were modified with several cysteine reagents. One of the five sulfhydryl groups reacts rapidly and specifically with N-ethylmaleimide without inactivation of the enzyme. Cysteine-116 was found to be the reactive cysteine by isolation of a labeled tryptic peptide. The enzyme is easily inactivated by mercurial compounds. The original activity can be fully restored by treatment of the modified enzyme with sulfhydryl-containing compounds. The rate of incorporation of mercurial compounds is pH-independent and is pseudo-first-order up to 90-95% loss of activity. The reaction shows saturation kinetics. The substrate p-hydroxybenzoate protects the enzyme from fast inactivation. The mercurial compounds themselves inhibit the inactivation reaction at concentrations higher than 80 microM. A spin-labeled derivative of p-chloromercuribenzoate reacts fairly specifically with only Cys-152 on use of enzyme prelabeled with N-ethylmaleimide, in contrast to p-chloromercuribenzoate which reacts with additional cysteine residues, i.e. Cys-211 and Cys-158. From these results it is concluded that modification of Cys-152 decreases drastically the affinity of the enzyme for the substrate. The results strongly indicate that the substrate binding site and Cys-152 are interdependent. This observation is not obvious when the three-dimensional data only are considered. The modified enzyme exhibits a somewhat higher affinity for NADPH than the native enzyme. Modification of N-ethylmaleimide-prelabeled enzyme by p-chloromercuribenzoate leads to absorbance difference spectra showing maxima at 250 nm, 290 nm and 360 nm. The intensities of the absorbance difference maxima at 290 nm and 360 nm are strongly dependent on the pH value of the solution. The intensities are very low at low pH values and increase with increasing pH values, reaching a maximum at about pH = 9. The ionizing group shows a pK value of about 7.6. The maximal molar difference absorption coefficient at 290 nm is 3200 M-1cm-1 at pH 9, suggesting that tyrosine residues ionize under the conditions of modification of the enzyme. The results are discussed in the light of the known three-dimensional structure.

Use of endoproteinase Lys-C from Lysobacter enzymogenes in protein sequence analysis.

Endoproteinase Lys-C from Lysobacter enzymogenes, which is commercially available, proved to be useful in the determination of primary structures of proteins. The enzyme preferentially cleaves at the carboxyl side of lysine residues.

p-Hydroxybenzoate hydroxylase from Pseudomonas fluorescens. 1. Completion of the elucidation of the primary structure.

As a final step in the elucidation of the primary structure of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens, the amino acid sequences of a CNBr peptide (CB1, positions 111-276), that accounts for the middle part of the sequence, and the C-terminal CNBr peptide (CB2, positions 277-394) from the enzyme were determined. Important sequence information was obtained from two subfragments that were formed by the cleavage with CNBr of the Met-Thr sequence (positions 346-347) in peptide CB2. The alignment of the two subfragments from peptide CB2 and three one-residue overlaps between peptides from one of these subfragments were confirmed by investigation of well-resolved parts of a 0.25-nm electron-density map. The sequence of residues 343-346 could not be determined with chemical methods and was assigned from the size and shape of the amino acids in the electron-density map. An important tool in the analysis of the amino acid sequence of peptide CB1 was the proteinase Lys-C from Lysobacter enzymogenes, which preferentially cleaves at lysine residues.

Primary structure of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens.

The amino acid sequence of the p-hydroxybenzoate hydroxylase (4-hydroxybenzoate,NADPH:oxygen oxidoreductase (3-hydroxylating), EC 1.14.13.2) monomer from Pseudomonas fluorescens has been determined. The sequence was elucidated by a combination of the results from an X-ray crystallographic study at 0.25 nm resolution (Wierenga, R.K., de Jong, R.J., Kalk, K.H., Hol, W.G.J. and Drenth, J. (1979) J. Mol. Biol. 131, 55-73) and from protein sequence analysis. The polypeptide chain of the monomer contains 394 amino acids and has a molecular weight of 44 299.

The amino acid sequence of hamster pancreatic ribonuclease.

The amino acid sequence of golden hamster pancreatic ribonuclease was determined by analysis of tryptic, chymotryptic, thermolytic, and CNBr peptides and by automatic sequence analysis of the intact protein. Like all RNases with an Asn-Met-Thr sequence at positions 34-36, hamster RNase is glycosylated at position 34 with a complex-type carbohydrated chain. Val-17, Ala-18, His-55, His-76 and Ala-90 have never been observed in other pancreatic RNases. Ala-90 replaces Ser-90, which had been invariant in all mammalian RNases studied so far. The amino acid sequence of hamster RNase differs at 15 positions from that of another Cricetidae rodent, the muskrat. The similarity between both ribonucleases was used to confirm a few less certain parts of the muskrat RNase sequence. The replacement rate of the RNases of the Cricetidae appeared to be higher than the average rate in the mammals, but much lower than the rate in another myomorph family, the Muridae (mouse and rat). Possibly, in many respects, the Cricetidae underwent less evolutionary change in recent times than the evolutionarily highly successful Muridae.