Single Basic Residue Research Articles

Role of potentially charged transmembrane residues in targeting proteins for retention and degradation within the endoplasmic reticulum.

The selective breakdown of newly synthesized proteins retained within the endoplasmic reticulum (ER) is probably mediated by the specific recognition of structural features of protein substrates by components of a degradative system. Within the alpha chain of the multisubunit T-cell antigen receptor (TCR) complex, a transmembrane sequence containing two basic amino acid residues has been shown to act as a determinant for retention and rapid degradation in the ER. We now demonstrate that single basic or acidic amino acid residues can cause targeting for retention and degradation in the ER when placed within the transmembrane domain of an integral membrane protein normally destined for the cell surface. The effect of such potentially charged residues is dependent on their relative position within the transmembrane sequence and on the nature of the amino acid side chains. The phenotypic changes induced by potentially charged transmembrane residues occur without apparent alterations of the global folding or transmembrane topology of the mutant proteins. These observations test the hypothesis that potentially charged residues within transmembrane domains can provide the basis for a motif for ER degradation and explain the selective breakdown of some proteins retained within the ER.

Membrane protein association by potential intrarnembrane charge pairs

The transmembrane domain of the alpha chain of the T-cell receptor is responsible both for its assembly with the CD3 delta chain and for rapid degradation of the unassembled chain within the endoplasmic reticulum. The determinant for both assembly and degradation is located in a segment of eight residues containing two basic amino acids. We show here that placement of a single basic residue in the transmembrane domain of the Tac antigen can induce interaction with the CD3 chain, through its transmembrane acidic residue. This interaction is most favoured when the interacting residues are located at the same level in the membrane. The ability to induce protein-protein interaction by placing charge pairs within transmembrane domains suggests an approach to producing artificial dimers.

Primary structure of the precursor for the sea anemone neuropeptide Antho-RFamide (less than Glu-Gly-Arg-Phe-NH2).

Neuropeptides containing the carboxylterminal sequence Arg-Phe-NH2 are found throughout the animal kingdom and are important substances mediating neuronal communication. Here, we have cloned the cDNA coding for the precursor protein of the sea anemone neuropeptide (Antho-RFamide) less than Glu-Gly-Arg-Phe-NH2. This precursor is 334 amino acids in length and contains 19 copies of unprocessed Antho-RFamide (Gln-Gly-Arg-Phe-Gly), which are tandemly arranged in the C-terminal part of the protein. Paired basic residues (Lys-Arg) or single basic residues (Arg) occur at the C-terminal side of each Antho-RFamide sequence. These are likely signals for posttranslational cleavage. The processing signals at the N-terminal side of each Antho-RFamide sequence, however, include acidic residues. Processing at these amino acids must involve either an amino- or an endopeptidase that cleaves C-terminally of aspartic acid or glutamic acid residues. Such processing is, to our knowledge, hitherto unknown for peptidergic neurons. The Antho-RFamide precursor also contains two copies of the putative Antho-RFamide-related peptide Phe-Gln-Gly-Arg-Phe-NH2 and one copy of Tyr-Val-Pro-Gly-Arg-Tyr-NH2. In addition, the precursor protein harbors four other putative neuropeptides that are much less related to Antho-RFamide. This report shows that the biosynthetic machinery for neuropeptides in coelenterates, the lowest animal group having a nervous system, is already very efficient and similar to that of higher invertebrates, such as mollusks and insects, and vertebrates.

Endopeptidases and prohormone processing

Peptide hormones and peptide transmitters are generated from polypeptide precursors by specific cleavage reactions which take place principally at sites formed by single or paired basic residues. Not all the possible cleavage sites are utilised, however, and the degree of processing of many propeptides has been found to vary according to the tissue of origin. The restricted nature of processing reactions could point to the existence of a series of enzymes with stringent specificities, recognising regions of structure in addition to the single or paired basic residues. Alternatively the action of processing enzymes may be directed by conformation of the pro-peptide which could focus the action of a protease onto or away from a particular site. In addition certain post-translational modifications such as glycosylation or phosphorylation may influence the accessibility of a site to the approach of a processing enzyme. In this review we describe recent advances that have been made in the characteristization of proteolytic processing enzymes, we examine the relevance of the various factors that could account for restricted processing and discuss new approaches that may lead to better understanding of the mechanisms involved.

Analysis of mutational alterations in the hydrophilic segment of the maltose-binding protein signal peptide.

Oligonucleotide-directed mutagenesis was employed to investigate the role of the hydrophilic segment of the Escherichia coli maltose-binding protein (MBP) signal peptide in the protein export process. The three basic residues residing at the amino terminus of the signal peptide were systematically substituted with neutral or acidic residues, decreasing the net charge in a stepwise fashion from +3 to -3. It was found that a net positive charge was not absolutely required for MBP export to the periplasm. However, export was most rapid and efficient when the signal peptide retained at least a single basic residue and a net charge of +1. The nature of the adjacent hydrophobic core helped to determine the effect of charge changes in the hydrophilic segment on MBP export, which suggested that these two regions of the signal peptide do not have totally distinct functions. Although the stepwise decrease in net charge of the signal peptide also resulted in a progressive decrease in the level of MBP synthesis, the data do not readily support a model in which MBP synthesis and export are obligately coupled events. The export defect resulting from alterations in the hydrophilic segment was partially suppressed in strains harboring certain prl alleles but not in strains harboring prlA alleles that are highly efficient suppressors of signal sequence mutations that alter the hydrophobic core.

Characterizing molecular heterogeneity of gastrin-releasing peptide and related peptides

Publisher Summary The characterization of multiple gastrin-releasing peptide molecular variants, and gene-related peptides, has been achieved utilizing region specific radioimmunoassays and high-resolution purification techniques. The posttranslational processing sites that yield these various forms are double basic residues and several other types of bonds. For example, processing occurs after second position prolines at the amino terminus, at single basic residues, and between aspartic and serine residues. Co-injections of similar amounts of synthetic and natural peptide should be done to avoid false conclusions about elution positions caused by variability in pump speed, chart recorder speed, or gradient formation. The various forms of gastrin-releasing peptide are well separated in several different chromatography systems. A combination of more than one separation technique is suggested to validate any conclusions about molecular forms based on immunoreactivity coeluting with standard peptides.

Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and OmpT

Escherichia coli cells were found to contain a novel outer membrane-associated protease, designated protease VII (K. Sugimura and N. Higashi, J. Bacteriol. 170:3650-3654, 1988). This enzyme was purified to homogeneity and exhibited an apparent molecular weight of 36,000 on sodium dodecyl sulfate gels and 180,000 on a TSK G-3000SW column in the presence of Triton X-100. It was capable of cleaving several peptides at the center of paired basic residues but not at single basic residues, implying that it is distinct from trypsinlike proteases. Protease VII was most active at pH 6.0 and was sensitive to a serine protease inhibitor, diisopropylfluorophosphate, and to the bivalent cations Zn2+, Cu2+, and Fe2+. The nucleotide sequence of a protease VII gene-carrying DNA fragment, which had been cloned by complementation analysis (K. Sugimura, Biochem. Biophys. Res. Commun. 153:753-759, 1988) was determined. It carried two putative promoter regions and a putative Shine-Dalgarno sequence in addition to the complete structural gene, which encoded pre-protease VII of 317 amino acid residues, with the N-terminal 20 residues being a signal peptide. By comparing their amino acid sequences, protease VII and OmpT, which specifically cleaves ferric enterobactin receptor protein, were found to be identical.

Processing of mammalian preprogastrin-releasing peptide.

The processing of preprogastrin-releasing peptide in mammalian tissues and in cultured cells takes place at discrete sites (Figure 6). Signal peptidase cleaves away the signal peptide from the amino terminus of gastrin-releasing peptide. An exopeptidase activity may remove dipeptides from the amino terminus. The amidation site (not shown in Fig. 6; see Fig. 2) has the same general sequence (Gly-Lys-Lys) seen for other amidated peptides. Cleavage after single basic residues yields gene-related products from Form I or II preproGRP. A unique non-basic cleavage yields a gene-related product from Form III preproGRP. The processing that occurs to form GRP, GRP, and GRP gene-related peptides is shown in Figure 7. ProGRP is cleaved by a series of enzymes to form GRP with an amidated carboxyl-terminal methionine (indicated by an asterisk in Fig. 7). GRP is cleaved to form the decapeptide GRP. The carboxyl-terminal flanking peptides of all three mRNA translation products are cleaved to form several gastrin-releasing peptide gene-related products. Knowledge of the processing of gastrin-releasing peptide and its gene-related products will allow synthesis of duplicates of the stored forms of these peptides, which can then be used for biological testing.

Processing of the oxytocin precursor: Isolation of an exopeptidase from neurosecretory granules of bovine pituitaries

The bovine pro-oxytocin precursor consists of the nonapeptide hormone and its neurophysin carrier protein that contains at its C-terminus a rudimentary processing signal, the single basic amino acid residue histidine. An exopeptidase has been isolated from neurosecretory granules of the bovine posterior pituitary that releases the supernumary histidine residue from the pro-hormone precursor. Based on its sensitivity to inhibitors and activators the enzyme has carboxypeptidase B-like properties with a pH optimum between 5.0 and 5.5.

Purification of an endopeptidase from bovine adrenal medulla granules which cleaves in vitro at paired but not at single basic residues

An endopeptidase was isolated from bovine adrenomedullary granules by fast protein liquid chromatography, including two ion exchange, one hydrophobic interaction, and one gel filtration step. The enzyme assay was based on the HPLC detection of the degradation of the dodecapeptide BAM 12P from the sequence of proenkephalin. After a 1200-fold purification, the enzyme fraction was homogeneous on polyacrylamide gel electrophoresis. The apparent molecular weight of the monomeric protein was 68,000 and its pH optimum was 5.6, in agreement with the internal pH of the granules. The specificity of the protease was determined initially by analysis of the degradation fragments of BAM 12P which showed that cleavage occurred at the double but not at the single Arg site of BAM 12P. The cleavage pattern of other substrates showed that the enzyme also recognized other pairs of basic amino acids. The behavior of the enzyme toward specific inhibitors showed that it was an acid thiol protease different from serine proteases and from lysosomal cathepsin B. The endopeptidase may act as a maturation enzyme in vivo.

Processing of mammalian preprogastrin releasing peptide

The processing of preprogastrin-releasing peptide in mammalian tissues and in cultured cells takes place at discrete sites (Figure 6). Signal peptidase cleaves away the signal peptide from the amino terminus of gastrin-releasing peptide. An exopeptidase activity may remove dipeptides from the amino terminus. The amidation site (not shown in Fig. 6; see Fig. 2) has the same general sequence (Gly-Lys-Lys) seen for other amidated peptides. Cleavage after single basic residues yields gene-related products from Form I or II preproGRP. A unique non-basic cleavage yields a gene-related product from Form III preproGRP. The processing that occurs to form GRP, GRP, and GRP gene-related peptides is shown in Figure 7. ProGRP is cleaved by a series of enzymes to form GRP with an amidated carboxyl-terminal methionine (indicated by an asterisk in Fig. 7). GRP is cleaved to form the decapeptide GRP. The carboxyl-terminal flanking peptides of all three mRNA translation products are cleaved to form several gastrin-releasing peptide gene-related products. Knowledge of the processing of gastrin-releasing peptide and its gene-related products will allow synthesis of duplicates of the stored forms of these peptides, which can then be used for biological testing.

Proteolytic processing of chromogranin A in purified insulin granules. Formation of a 20 kDa N-terminal fragment (betagranin) by the concerted action of a Ca2+-dependent endopeptidase and carboxypeptidase H (EC 3.4.17.10).

The nature and subcellular localization of the enzymic activities responsible for the production of the 20 kDa protein betagranin from its 100 kDa chromogranin-A-like precursor was investigated in transplantable insulinoma tissue. [35S]Methionine-labelled precursor was converted by lysed insulin-secretory granules into betagranin and one or more proteins of 47 kDa, via intermediates in the 60-65 kDa range. Lysosome-enriched fractions also processed the precursor, but not into the peptides found in vivo; other fractions, including those enriched in Golgi, were inactive. Conversion of the precursor by granules was quantitative and the products were stable. Inhibitor studies showed that processing occurred by initial endoproteolytic cleavage at sites marked by pairs of basic amino acids, followed by removal of these by carboxypeptidase H. The endopeptidase activity appeared to be a novel metalloenzyme, with a markedly acidic pH optimum (4.8-5). It was inhibited by alanyl-L-lysyl-L-arginyl chloromethane (K0.5 = 1.3 microM), but to a much lesser extent by inhibitor analogues of processing sites defined by single or unpaired basic amino acid residues, e.g. alanyl-L-norleucyl-L-arginylchloromethane (K0.5 greater than 100 microM), leupeptin (K0.5 = 150 microM) and antipain (K0.5 = 40 microM). p-Chloromercuribenzoate (K0.5 = 13 microM), Hg2+ (K0.5 = 16 microM), Zn2+ (K0.5 = 0.8 mM) and vanadate (K0.5 = 7 microM) also abolished activity, as did various anions (SCN- greater than I- greater than Cl- greater than SO4(2-). Group-specific inhibitors of serine, thiol and acidic endopeptidases were without effect. EDTA and CDTA (1,2-cyclohexanediaminetetra-acetic acid), but not 1,10-phenanthroline, abolished endoproteolytic activity. Several bivalent cations could restore activity after EDTA or CDTA inhibition, including Ca2+, Zn2+, Mn2+ and Sr2+; however, the ion of physiological importance appeared to be Ca2+ (K0.5 = 8 microM). The properties of the granule endopeptidase and its subcellular localization suggested that it is of importance in processing chromogranin A in the pancreatic beta-cell.

Structural comparison of the cleavage-activation site of the fusion glycoprotein between virulent and avirulent strains of newcastle disease virus

The nucleotide sequence of the mRNA encoding the fusion (F 0) protein of a virulent strain of Newcastle disease virus was determined. A single open reading frame in the sequence encodes a protein of 553 amino acids with a calculated molecular weight of 59058. The amino acid sequence predicted several structural features involving the fusion-inducing hydrophobic stretch (residues 117–142) and the cleavage-activation site (residues 112–116) to generate the disulfide-linked F 1 and F 2 subunits. The cleavage-activation site as well as a part of the fusion-inducing sequence were compared among a series of virulent and avirulent strains by the chain-termination method using a synthetic oligonucleotide primer. It was found that without exception, the cleavage-activation site of virulent strains consisted of two dibasic residues with an intervening glutamine, Arg-Arg-Gln-Arg-Arg, whereas the corresponding region of avirulent strains was made of a sequence with single basic residues scattered among uncharged residues, Gly- Lys Arg-Gln- Gly Ser-Arg On the basis of these observations and the previous results showing a strict correlation between the pathogenicity and the cleavability of the fusion protein of NDV (Y. Nagai, H-D. Klenk, and R. Rott, Virology, 72, 494–508, 1976), we propose the importance of the dibasic residues for efficient proteolytic activation of the fusion protein and for the pantropic property of NDV. Some strains were found to have Leu-Ile-Gly as the N-terminus of F 1, whereas others contained Phe-Ile-Gly, indicating that Phe-X-Gly is not always conserved at F, N-terminus of paramyxovirus.

New molecular forms of cholecystokinin. Microsequence analysis of forms previously characterized by chromatographic methods.

Cholecystokinin previously has been characterized by chromatographic and immunological techniques. Analysis of cDNA has revealed the structure of preprocholecystokinin. The predicted processing sites of preprocholecystokinin cannot account for the multiple forms of cholecystokinin detected. This report details the isolation and characterization of cholecystokinin peptides containing 58, 39, 33, 25, 18, 8, 7, and 5 amino acids. None of the cleavages that occurred to form these peptides was at the carboxyl side of double basic residues. Cholecystokinin 25, 18, and 7 have not previously been isolated and identified by sequence analysis. The processing that forms these peptides includes cleavage after single basic residues for the 58, 39, 33, and 8 amino acid peptides. The 25, 18, 7, and 5 amino acid peptides must be formed by other endopeptidases or combinations of endo- and exopeptidases. The analysis of this series of peptides provides the chemical basis for structural differences in cholecystokinin molecules previously demonstrated by chromatographic and immunological methods. These structures provide insight into tissue-specific processing that occurs for this important regulatory peptide in intestine and brain.

An endopeptidase associated with bovine neurohypophysis secretory granules cleaves pro-ocytocin/neurophysin peptide at paired basic residues

The octacosapeptide sequence [Tyr 18] pro-ocytocin/neurophysin (1–18)NH 2 [ pro-OT Np(1–18)NH 2 ] was synthesized and used as substrate to detect endoprotease(s) possibly involved in the processing of this precursor in bovine hypothalamo-neurohypophyseal tract. An endopeptidase (58 Kda) was detected in lysates made from highly purified neurosecretory granules. This protease which cleaves the peptide bond on the carboxyl side of the Lys-Arg doublet, and no single basic residue, generates both OT-Gly 10-Lys 11-Arg 12+Ala 13-Val-Leu-Asp-Leu-Tyr 18(NH 2) from the octacosapeptide substrate. In addition, a carboxypeptidase B-like activity converting OT-Gly 10-Lys 11-Arg 12 into OT-Gly 10 was detected in the same granule lysates. It is hypothesized that a combination of these endoprotease and carboxypeptidase B-like activities together with the amidating enzyme of secretory granules might participate in the cleavage and processing of pro-OT Np in vivo .

Characterization of endorphins from the pituitary of the Spiny Dogfish Squalus acanthias

Opioid-like immunoreactive material was extracted from the pituitary and brain of the Spiny Dogfish Shark Squalus acanthias. The immunoreactive material in the pituitary extracts was purified to apparent homogeneity by reverse phase high performance liquid chromatography and subsequently characterized by amino acid analysis, Edman degradation and fast atom bombardment mass spectrometry. The largest opioid-like peptide isolated contained 30 amino acids and showed 80 percent homology with salmon endorphin-II but less than 50 percent homology with human β-endorphin. Three structural variants of this molecule were also characterized. These variants were shown to be shorter N-terminal fragments, two of which corresponded to cleavage products at the single basic residues arginine 11 and lysine 26. Cleavage at a single lysine residue has not been reported for posttranslational processing of β-endorphin in mammals and could represent a modification seen only in lower vertebrates. The remaining fragment corresponded to a loss of 3 residues from the C-terminus of the parent molecule. No α-N-acetylated peptides were detected. These results provide the first unequivocal confirmation of β-endorphin in an elasmobranch and provide evidence of novel N-terminal variants of β-endorphin.

A putative prohormone processing protease in bovine adrenal medulla specifically cleaving in between Lys-Arg sequences

Paired basic residues, particularly Lys-Arg, are known as a typical site for proteolytic processing of prohormones. In this study, we confirmed the presence of a novel protease exhibiting substrate specificity toward Lys-Arg sequence. It was partially purified from the soluble fraction of bovine adrenomedullary chromaffin granules by using an affinity chromatography on soybean trypsin inhibitor-Sepharose. The enzyme, with optimal pH around 7.5–9.5, is classified into a serine-protease family by its inhibition spectrum. The enzyme specifically cleaves in between the Lys-Arg bonds of the peptides related to proenkephalins, but the sequences of Arg-Arg, Arg-Lys and a single basic residue (Arg or Lys) in the substrates are not affected by the enzyme. The unique substrate specificity of the enzyme suggests that it is distinct from pancreatic trypsin and may be physiologically involved in proenkephalin processing.

Proenkephalin processing enzyme with specificity toward paired basic residues purified from bovine adrenal chromaffin granules

A novel protease exhibiting substrate specificity toward paired basic residues has been partially purified from the soluble fraction of bovine adrenal chromaffin granules by utilizing an affinity chromatography on STI-Sepharose. The enzyme, with optimal pH around 7.5–9.5, is classified into a serine-protease by its inhibitor spectrum. The enzyme specifically cleaved the Lys-Arg bonds of two synthetic peptides containing the subsequence of proenkephalin A, but endogenous opioid peptides containing a single basic residue in the molecule ((Met)enk-Arg-Phe, (Met)enk-Arg-Gly-Leu) were not affected by the enzyme. The unique substrate specificity of the enzyme, which is well in accord with the processing pattern of proenkephalin A in adrenal medulla, indicates that the enzyme may be physiologically involved in proenkephalin processing.

Hormone processing and membrane-bound proteinases in yeast.

A search for maturating peptidases of the precursor protein of the mating hormone (pheromone) alpha-factor of Saccharomyces cerevisiae was performed using short model peptides representing those sequences of the precursor protein, where cleavage is thought to occur in vivo. This search was done in a mutant lacking several of the unspecific vacuolar peptidases. The chromogenic peptide Cbz-Tyr-Lys-Arg-4-nitroanilide led to the detection of a membrane-bound enzyme called proteinase yscF. Cleavage of the synthetic peptide derivative occurs after the basic amino acid pair, a proposed signal for hormone processing. Optimum pH for the reaction is 7.2. The enzyme does not cleave after single basic amino acid residues indicating that it is distinct from trypsin-like proteinases. Proteolytic activity is enhanced by Triton X-100. The enzyme is strongly inhibited by EGTA, EDTA and mercurials but insensitive to phenylmethylsulfonyl fluoride. The enzyme activity is strongly dependent on Ca2+ ions. In a mutant (kex2), which accumulates an over-glycosylated alpha-factor precursor, no proteinase yscF activity can be found. Membrane-bound peptidase activity possibly involved in removal of the arginyl and lysyl residues remaining at the carboxy terminus of the alpha-factor pheromone peptide after the initial cut of the precursor molecule could be identified by using the model peptides Cbz-Tyr-Lys-Arg and Cbz-Tyr-Lys.

Abnormal lecithin:cholesterol acyltransferase activation by a human apolipoprotein A-I variant in which a single lysine residue is deleted.

An apolipoprotein (apo) A-I variant that has a relative charge of -1 compared to normal apo-A-I on isoelectric focusing gels has been identified in five unrelated families as a result of screening a large number of individuals. The cause of the electrophoretic abnormality has been examined by analyzing the variant apo-A-I structure. The evidence suggests that a single amino acid, lysine 107, has been deleted in the variant apo-A-I of all affected individuals studied from these families, with the remainder of the variant apo-A-I sequence being unaffected. The deletion of this single basic amino acid residue is sufficient to account for the charge difference between the variant and normal apo-A-I as seen on isoelectric focusing gels. This variant, previously referred to as A-I-Marburg or A-I-Münster-2, can now be designated by the structural abnormality apo-A-I(Lys107----0). The evidence from extensive pedigree analysis suggests the likelihood that the deletion mutant gene is allelic to the normal apo-A-I gene. At the same time, the kindred analyses have failed to yield a lipid abnormality that can be unequivocally related to the presence of this deletion mutant of apo-A-I. However, all subjects expressing apo-A-I(Lys107----0) also express normal apo-A-I, so that any abnormality caused by the variant apo-A-I might be adequately compensated for by the normal apo-A-I. To examine directly the functional consequence of the lysine deletion, the isolated variant was tested in vitro for its ability to activate lecithin:cholesterol acyltransferase, the principal cholesterol-esterifying enzyme in plasma. It was found that apo-A-I(Lys107----0) is deficient in its ability to activate lecithin:cholesterol acyltransferase, having only 40-60% of the cofactor activity of normal apo-A-I. The cofactor activity of the pro-apo-A-I component of the variant was also reduced to about 60% of either normal A-I or normal pro-apo-A-I. The functional defect is probably related to a disruption in the secondary and/or tertiary structure of the protein caused by the deletion of lysine 107 in the primary structure.