The general mitochondrial matrix processing protease from rat liver: structural characterization of the catalytic subunit.

A critical step in the import of nuclear-encoded precursor proteins into mitochondria involves proteolytic cleavage of their amino-terminal leader peptides by processing proteases found in the mitochondrial matrix. We report here the characterization of the general matrix processing protease from rat liver mitochondria. The final enzyme preparation consisted of two polypeptides, a catalytically active 55-kDa subunit and a 52-kDa one. To deduce the complete primary structure of the 55-kDa subunit, we first sequenced its mature amino terminus and several tryptic peptides derived from the pure protein. Next, using mixed oligonucleotide primers that had sequences based on two of these peptides, we synthesized a partial cDNA probe by selective amplification of liver RNA with the polymerase chain reaction. The amplified probe was then used to obtain a nearly full-length clone from a rat liver cDNA library. This cDNA codes for 508 amino acid residues, including 16 residues of an amino-terminal leader peptide, the cleavage site of which is located two polypeptide bonds downstream from an arginine residue. The mature portion has a predicted molecular mass of 55.2 kDa; it shows 36% identity with the mitochondrial processing peptidases of Saccharomyces cerevisiae and Neurospora crassa. A conserved structural feature is a putative, negatively charged alpha-helix, located in the amino-terminal half of the subunit; this element might be important for the recognition of positively charged leader peptides characteristic of mitochondrial precursor proteins.     

Cloning of cDNA encoding the pre-beta subunit of mouse thyrotropin.

Double-stranded cDNA was synthesized from sucrose gradient-purified poly(A)+ mRNA from a mouse thyrotropic tumor, inserted into the Pst I site of plasmid pBR322 by using poly(dC) . poly(dG) homopolymeric extensions, and cloned in Escherichia coli RRI. Plasmids containing cDNA sequences coding for the beta subunit of thyrotropin (TSH) were identified by cell-free translation of hybrid-selected mRNA and immunoprecipitation with specific antibody to TSH beta subunit. Determination of the nucleotide sequence of one cDNA, 595 base pairs in length, allowed us to deduce the entire amino acid sequence of the mouse TSH beta subunit. The pre-beta subunit contains a 20-amino acid amino-terminal signal sequence followed by a 118-amino acid mature TSH beta subunit. There is 85-90% homology in amino acid sequence between mouse TSH beta subunit and subunits from man, pig, and cow; however, the mouse subunit contains an additional 5 or 6 amino acids at its carboxyl terminus compared to the bovine or human and pig subunits, respectively. TSH beta-subunit mRNA from mouse thyrotropic tumor was estimated to be 750 nucleotides in length by hybridization with labeled TSH beta-subunit cDNA.     

Sequence analysis of rat mitochondrial intermediate peptidase: similarity to zinc metallopeptidases and to a putative yeast homologue.

Proteolytic removal of amino-terminal octapeptides from mitochondrial intermediate proteins is a required step for a subgroup of nuclear-encoded mitochondrial precursors and is specifically catalyzed by mitochondrial intermediate peptidase (MIP). We recently reported the purification of MIP from rat liver and showed that the enzyme is a monomer of 75 kDa. We now report the sequence of a full-length rat MIP cDNA. This cDNA codes for a protein of 710 amino acids, including an amino-terminal mitochondrial leader peptide of 33 residues. The region surrounding the mature MIP amino terminus shows a cleavage site typically recognized by the general mitochondrial processing peptidase (MPP). In vitro synthesized MIP precursor is cleaved to mature MIP by purified MPP, and thus MIP is not required for its own proteolytic maturation. Comparison of the deduced MIP sequence with other sequences in the GenBank data base reveals two important similarities. The first is to a sequence encoding a putative MIP homologue in the recently reported sequence of yeast chromosome III. The putative yeast protein is predicted to be 712 amino acids long and includes a putative 23-residue mitochondrial leader peptide also with a MPP processing site. It shows 47% similarity and 24% identity to rat MIP. The second similarity is to members of a subfamily of metallopeptidases that includes rat metalloendopeptidase EC 3.4.24.15 and two bacterial proteases, oligopeptidase A and dipeptidyl carboxypeptidase. A region of greater than 50% similarity over 400 residues between MIP and these proteins is centered around the sequence motif HEXXH, typical of zinc metallopeptidases.     

Subunits of purified calcium channels: a 212-kDa form of alpha 1 and partial amino acid sequence of a phosphorylation site of an independent beta subunit.

Antibodies prepared against peptides CP2, CP4, and CP5, which occur within the first 1522 amino acid residues of the alpha 1 subunit of dihydropyridine-sensitive skeletal muscle calcium channels, specifically recognized a 175-kDa form of the alpha 1 subunit in immunoblots and immunoprecipitation experiments. In contrast, antibodies prepared against peptide CP1, which represents the C-terminal 18 amino acid residues predicted by cloning and sequence analysis of the alpha 1 subunit, recognized a minor, previously undescribed 212-kDa protein, which is the size predicted for the full length of the alpha 1 subunit from cDNA cloning [Tanabe, T., Takeshima, H., Mikami, A., Flockerzi, V., Takahashi, H., Kangawa, K., Kojima, M., Matsuo, H., Hirose, T. & Numa, S. (1987) Nature (London) 328, 313-318]. Both the 175-kDa and 212-kDa forms were phosphorylated by cAMP-dependent protein kinase and both were present in isolated transverse tubule membranes. The 175-kDa form may arise from posttranslational proteolytic cleavage of the C terminus of the 212-kDa form of the alpha 1 subunit predicted by cDNA cloning and sequence analysis. Partial amino acid sequencing of the 54-kDa beta subunit of the calcium channel indicated this protein was not derived from the proteolytically cleaved C terminus of the alpha 1 subunit. This analysis identified a threonine residue in the sequence (Lys/Arg)-Arg-Pro-Thr-Pro of the beta subunit that was phosphorylated by cAMP-dependent protein kinase. Phosphorylation of this residue in the beta subunit may play a role in modulation of calcium channel function. Separate functional roles of the 175-kDa form of the alpha 1 subunit in excitation-contraction coupling and of the 212-kDa form in ion conductance are proposed.     

The alpha and beta chains of human platelet glycoprotein Ib are both transmembrane proteins containing a leucine-rich amino acid sequence.

The primary structure of the beta chain of human glycoprotein Ib (GPIb), the platelet receptor for von Willebrand factor, has been established by a combination of cDNA cloning and amino acid sequence analysis. A lambda phage cDNA expression library prepared from human erythroleukemia cells (HEL cells) was screened with a radiolabeled affinity-purified rabbit polyclonal antibody to the beta chain of GPIb. Eighteen positive clones were isolated and plaque-purified and the nucleotide sequences of three were determined. The composite sequence spanned 968 nucleotides and included a 5' untranslated region of 22 nucleotides, an open reading frame of 618 nucleotides encoding a signal peptide of 28 amino acids and a mature protein of 181 amino acids, a stop codon, and a 3' noncoding region of 307 nucleotides. The 3' noncoding sequence also contained a polyadenylylation signal (AATAAA) 14 nucleotides upstream from the poly(A) tail of 18 nucleotides. Edman degradation of the intact beta chain and of peptides produced by chemical cleavage yielded amino acid sequences spanning 76 residues that were identical to those predicted from the cDNA. The amino-terminal region of the beta chain contains a leucine-rich sequence of 24 amino acids that is similar to a sequence that occurs as seven tandem repeats in the alpha chain of GPIb and nine tandem repeats in leucine-rich alpha 2-glycoprotein. The leucine-rich sequence in the beta chain of GPIb is flanked on both sides by amino acid sequences that are similar to those flanking the leucine-rich tandem repeats of the alpha chain of GPIb and leucine-rich alpha 2-glycoprotein. The amino-terminal region of the beta chain of GPIb is followed by a transmembrane segment of 25 amino acids and an intracellular segment of 34 amino acids at the carboxyl terminus of the protein. The intracellular segment contains an unpaired cysteine and two potential sites for phosphorylation by cAMP-dependent protein kinase.     

Molecular cloning of cDNA coding for the gamma subunit of Torpedo acetylcholine receptor.

From the electric organ of Torpedo californica, we purified mRNA that, when translated in vitro, produces polypeptides immunoprecipitable by antibodies against purified acetylcholine receptor. A novel cloning system [Okayama, H. & Berg, P. (1982) Mol. Cell. Biol. 2, 161-170] was used to produce a cDNA library from this mRNA. This library contained clones with receptor sequences identified by differential hybridization and hybridization-selection. We describe a clone of 2,030 base pairs with sequences appropriate for the amino-terminal amino acids of the gamma subunit of acetylcholine receptor. This clone contains 82 bases 5' of the codon for the amino-terminal amino acid of the mature protein. A portion of this sequence codes for a methionine followed by a 16-amino acid polypeptide that is contiguous to the amino-terminal amino acid of the mature protein and that has the characteristics of a leader peptide. The cDNA insert hybridizes to a 2,100-base RNA present in electric organ but not in the brain of T. californica.     

Molecular characterization of the murine cytotoxic T-cell membrane glycoprotein Ly-3 (CD8)

The murine Ly-2/3 glycoprotein is a surface marker of T cells restricted by class I major histocompatibility complex antigens. It is a disulfide-bonded heterodimer in which either the alpha or alpha' polypeptide chain encoded by Ly-2 is covalently linked to the beta polypeptide chain encoded by Ly-3. The nucleotide and predicted amino acid sequence of the murine Ly-3 cDNA, isolated by using the rat Ly-3 cDNA clone pX9.15, together with the amino acid sequence of Ly-3.1 peptides and the N terminus, are presented here. The alignment of peptide data from the Ly-3.1 antigen with that of the predicted amino acid sequence of the Ly-3.2 antigen confirmed that the putative Ly-3 cDNA clones do in fact encode the Ly-3 protein. The Ly-3.2 cDNA clones encode a protein of 213 amino acids, which includes a 21-residue leader sequence and structural features in common with immunoglobulin variable, joining, and hinge regions. Searches of protein data bases revealed that Ly-3 is a member of the immunoglobulin superfamily with significant homology to Ly-2, immunoglobulin variable region kappa and lambda light chains, and the beta chain of the T-cell receptor. A single N-linked glycosylation site was found at asparagine-13. The relative expression of two mRNA species (approximately 1.3 and 2.3 kilobases) varied according to the source of mRNA. A murine B1 repeat was located in the 3' untranslated region of Ly-3 cDNA clones.     

Amino acid and cDNA sequences of a vascular endothelial cell mitogen that is homologous to platelet-derived growth factor.

Glioma-derived vascular endothelial cell growth factor (GD-VEGF) is a 46-kDa dimeric glycoprotein mitogen with apparently greater specificity for vascular endothelial cells than the well-characterized fibroblast growth factors. The GD-VEGF cDNA sequence encodes a 190-amino acid residue subunit that is converted, by removal of an amino-terminal hydrophobic secretory leader sequence, to the mature 164-residue subunit characterized by direct amino acid sequencing. The GD-VEGF homodimeric subunit is homologous to the platelet-derived growth factor A and B chains and its oncogene homologue v-sis.     

Identification of a mouse brain cDNA that encodes a protein related to the Alzheimer disease-associated amyloid beta protein precursor.

We have isolated a cDNA from a mouse brain library that encodes a protein whose predicted amino acid sequence is 42% identical and 64% similar to that of the amyloid beta protein precursor (APP). This 653-amino acid protein, which we have termed the amyloid precursor-like protein (APLP), appears to be similar to APP in overall structure as well as amino acid sequence. The amino acid homologies are concentrated within three distinct regions of the two proteins where the identities are 47%, 54%, and 56%. The APLP cDNA hybridizes to two messages of approximately 2.4 and 1.6 kilobases that are present in mouse brain and neuroblastoma cells. Polyclonal antibodies raised against a peptide derived from the C terminus of APLP stain the cytoplasm in a pattern reminiscent of Golgi staining. In addition to APP, APLP also displays significant homology to the Drosophila APP-like protein APPL and a rat testes APP-like protein. These data indicate that the APP gene is a member of a strongly conserved gene family. Studies aimed at determining the functions of the proteins encoded by this gene family should provide valuable clues to their potential role in Alzheimer disease neuropathology.     

Isolation of a cDNA clone encoding pancreatic polypeptide.

We have isolated a cDNA clone encoding pancreatic polypeptide from a cDNA library constructed with RNA from an endocrine neoplasm of the human pancreas. The cDNA was inserted into plasmid pBR322 and the plasmid was cloned in Escherichia coli. Oligonucleotides (sequence in text) specific for the amino acid sequence (sequence in text) of pancreatic polypeptide were used as hybridization probes. The pancreatic polypeptide cDNA isolated was 465 base pairs long and encoded a peptide of 95 amino acids in the coding region. The 36-amino acid sequence of pancreatic polypeptide was flanked by a 29-amino acid putative leader sequence at the amino terminus and a connecting tripeptide (Gly-Lys-Arg) followed by a 27-amino acid peptide at the carboxyl terminus. The first 20 of the amino acids in the carboxyl-terminal heptacosapeptide were identical to the structure of human pancreatic icosapeptide with the single exception of an isoleucine substitution for valine in the 18th position. This alteration results from an A----G substitution in the nucleotide sequence of the cDNA and may represent a genetic variation or a point mutation in the pancreatic polypeptide cDNA.     

Molecular cloning of cDNAs for precursors of porcine pituitary glycoprotein hormone common alpha-subunit and of thyroid stimulating hormone beta-subunit

cDNA clones encoding precursors of glycoprotein hormone common alpha-subunit (pre-alpha) and of thyroid stimulating hormone beta-subunit (pre-TSH beta) were isolated from a porcine anterior pituitary cDNA library using DNA probes, and the nucleotide sequences were determined. The nucleotide sequence of pre-alpha cDNA contained an entire coding region (360 bases) including 5' and 3' untranslated regions. The pre-alpha mRNA was about 900 bases long. The predicted amino acid sequence consisted of a signal peptide of 24 amino acid residues and a mature alpha-subunit protein of 96 residues. Six amino acid residues at the amino terminus of the predicted mature protein had not been found by direct amino acid sequencing of the purified protein. The nucleotide sequence of pre-TSH beta cDNA contained an entire coding region and a 3' untranslated region which has two polyadenylation signals. The length of the pre-TSH beta mRNA was about 500 bases long. The predicted amino acid sequence consisted of a signal peptide of 20 amino acid residues, a mature protein of 112 residues and an additional extension of six amino acid residues at the carboxyl terminus, which had not been found in the amino acid sequence of the purified protein. The coding sequences of the cDNAs showed high homologies with those of other mammalian species (84-93% for pre-alpha and 81-94% for pre-TSH beta). Comprehensive data of our serial molecular cloning for porcine glycoprotein hormones revealed low but significant homologies (34-40%) among three beta-subunits. Upon comparison of frequency of (U)n A sequence in 3' untranslated region, porcine pre-alpha and pre-TSH beta mRNAs were grouped into a moderate class of mRNA stability whereas porcine pre-FSH beta and pre-LH beta were grouped into unstable and stable classes, respectively.     

Cloning and cDNA sequence of the dihydrolipoamide dehydrogenase component human alpha-ketoacid dehydrogenase complexes.

cDNA clones comprising the entire coding region for human dihydrolipoamide dehydrogenase (dihydrolipoamide:NAD+ oxidoreductase, EC 1.8.1.4) have been isolated from a human liver cDNA library. The cDNA sequence of the largest clone consisted of 2082 base pairs and contained a 1527-base open reading frame that encodes a precursor dihydrolipoamide dehydrogenase of 509 amino acid residues. The first 35-amino acid residues of the open reading frame probably correspond to a typical mitochondrial import leader sequence. The predicted amino acid sequence of the mature protein, starting at the residue number 36 of the open reading frame, is almost identical (greater than 98% homology) with the known partial amino acid sequence of the pig heart dihydrolipoamide dehydrogenase. The cDNA clone also contains a 3' untranslated region of 505 bases with an unusual polyadenylylation signal (TATAAA) and a short poly(A) track. By blot-hybridization analysis with the cDNA as probe, two mRNAs, 2.2 and 2.4 kilobases in size, have been detected in human tissues and fibroblasts, whereas only one mRNA (2.4 kilobases) was detected in rat tissues.     

Cloning of complimentary deoxyribonucleic acid encoding follicle-stimulating hormone and luteinizing hormone beta subunit precursor molecules in Reeves's turtle (Geoclemys reevesii) and Japanese grass lizard (Takydromus tachydromoides)

Reptilia is the only vertebrate class in which cDNA for the gonadotropin beta subunit precursor molecule has not been cloned. We have isolated the full-length cDNA clone encoding the LH beta subunit precursor molecule and a partial cDNA clone encoding the FSH beta subunit precursor molecule from a pituitary cDNA library of Reeves's turtle. We further clarified the nucleotide sequence of the remaining part of the turtle FSH beta cDNA and that of full-length cDNA encoding the LH beta subunit precursor molecule of the Japanese grass lizard, by means of the 5' rapid amplification of cDNA end (RACE) and 3' RACE. The nucleotide sequence of the turtle FSH beta cDNA we determined was 584 bp long and contained the coding sequence, 5' untranslated region (UTR) and 3' UTR of 396, 34, and 154 bp, respectively. The nucleotide sequence of the turtle LH beta we isolated was 498 bp long and contained the coding sequence, 5' UTR and 3' UTR of 420, 7, and 71 bp, respectively. The nucleotide sequence of the lizard LH beta we determined was 537 bp long and contained the coding sequence, 5' UTR and 3' UTR of 441, 35, and 61 bp, respectively. Amino acid sequences deduced from coding regions of the turtle FSH beta, LH beta and the lizard LH beta were 131, 139, and 146 residues, respectively. Referring to the amino acid sequences of the bullfrog FSH and LH beta subunit molecules determined chemically, we deduced the amino acid sequences of mature peptide. Amino acid sequences of mature peptides of the turtle FSH, turtle LH, and the lizard LH were 111, 112, and 112 residues, respectively. Amino acid sequences of the mature peptides were compared with those of other vertebrates. The amino acid sequence of the turtle FSH beta subunit molecule was 84.7-85.6, 67.8-71.4, and 61.3-62.2% identical to the FSH sequence of birds, mammals, and amphibians, respectively. The amino acid sequence of the turtle LH beta subunit molecule was 51.6-54.6, 36.2-48.7, and 56.3-57.5% identical to the LH sequence of birds, mammals, and amphibians, respectively. The amino acid sequence of the lizard LH beta subunit molecule was 39.1-47.1, 32.9-43.0, and 46.0-47.3% identical to the LH sequence of birds, mammals, and amphibians, respectively. These identity values suggest that the turtle or reptilian FSH beta subunit molecule is more closely related to avian and mammalian FSH beta subunit molecules than to amphibian FSH beta subunit molecules but reptilian LH beta subunit molecules are more closely related to amphibian LH beta subunit molecules than to avian and mammalian LH beta subunit molecules. This discrepancy in the molecular similarity relationship found in the reptilian FSH and LH beta subunit molecules can be interpreted by assuming that evolution speed was not the same among hormone species and also among vertebrate groups.     

Cloning and characterization of cDNAs encoding the complete sequence of decay-accelerating factor of human complement.

cDNAs encoding the complement decay-accelerating factor (DAF) were isolated from HeLa and differentiated HL-60 lambda gt cDNA libraries by screening with a codon preference oligonucleotide corresponding to DAF NH2-terminal amino acids 3-14. The composite cDNA sequence showed a 347-amino acid protein preceded by an NH2-terminal leader peptide sequence. The translated sequence beginning at the DAF NH2 terminus encodes four contiguous approximately equal to 61-amino acid long repetitive units of internal homology. The repetitive regions contain four conserved cysteines, one proline, one glycine, one glycine/alanine, four leucines/isoleucines/valines, one serine, three tyrosines/phenylalanines, and one tryptophan and show striking homology to similar regions previously identified in factor B, C2, C4 binding protein, factor H, C1r, factor XIII, interleukin 2 receptor, and serum beta 2-glycoprotein I. The consensus repeats are attached to a 70-amino acid long segment rich in serine and threonine (potential O-glycosylation sites), which is in turn followed by a stretch of hydrophobic amino acids. RNA blot analysis of HeLa and HL-60 RNA revealed three DAF mRNA species of 3.1, 2.7, and 2.0 kilobases. The results indicate that portions of the DAF gene may have evolved from a DNA element common to the above proteins, that DAF cDNA predicts a COOH-terminal anchoring polypeptide, and that distinct species of DAF message are elaborated in cells.     

Molecular cloning of complementary DNAs encoding two cationic peroxidases from cultivated peanut cells.

We have isolated, cloned, and characterized two cDNAs corresponding to the mRNAs for cationic peroxidases synthesized by cultured peanut cells. The first clone was obtained from a phage lambda gt11 library screened with antibodies directed against the major secreted isozyme. Its predicted amino acid sequence, deduced from the 1228-base-pair (bp) cDNA, revealed a 22-amino acid signal peptide and a 294-amino acid mature protein (Mr, 31,228). The second clone was isolated from a lambda gt10 library screened with oligonucleotides corresponding to the regions for acid/base catalysis and the fifth ligand of heme. This cDNA (1344 bp) encodes a protein (330 amino acids) with a mature peptide of 307 residues (Mr, 32,954). The two peanut peroxidases are 46% homologous. The estimated gene copy numbers of these peroxidases might be close to 1 or 2 per haploid genome. A comparison of the amino acid sequence of these peanut peroxidases with other known isozymes shows two already known regions of homology (the region for acid/base catalysis and the fifth ligand of heme). Moreover, some new characteristics appeared such as a glycosylation site identical in five of the seven isozymes, a putative antigenic determinant common to all the isozymes, and a region of the highest homology. A secondary structure prediction showed that it corresponds to a 16-amino acid helix linked to the next one by a long stretch of beta strands and coils and might represent a critical structural element.     

Human alpha-galactosidase A: nucleotide sequence of a cDNA clone encoding the mature enzyme.

The complete nucleotide sequence has been determined for a lambda gt11 cDNA clone (lambda AG18) containing the full-length coding region for the mature lysosomal form of human alpha-galactosidase A (alpha-Gal A; EC 3.2.1.22). The lambda AG18 insert contained a 1226-base-pair sequence with an open reading frame encoding 398 amino acids of the mature polypeptide (predicted Mr = 45,356) and the last 5 amino acids of the propeptide sequence. The poly(A) signals AATACA and ATTAAA occurred 28 and 11 nucleotides prior to the TAA stop codon, respectively. There was no 3' untranslated region as the poly(A) sequence immediately followed the TAA termination codon; a second independently cloned cDNA confirmed this finding. The predicted amino acid sequence was colinear with 86 nonoverlapping residues (22% of the mature subunit) determined by microsequencing amino-terminal, tryptic, and cyanogen bromide peptides of the purified mature enzyme. Four potential N-glycosylation sites were identified, all of which occurred at predicted beta turns in hydrophilic regions of secondary structure. RNA transfer hybridization analysis of HeLa poly(A)+ RNA demonstrated a single 1.45-kilobase band whose signal was decreased by prior immunoabsorption of polysomes with monospecific alpha-Gal A antibodies. Searches of nucleic acid and protein data bases did not reveal significant homology even with the limited sequences available for mammalian lysosomal enzymes.     

Molecular cloning and characterization of cDNA encoding the alpha subunit of the rat protein synthesis initiation factor eIF-2B.

Eukaryotic initiation factor 2B (eIF-2B) is an essential component of the pathway of peptide-chain initiation in mammalian cells, yet little is known about its molecular structure and regulation. To investigate the structure, regulation, and interactions of the individual subunits of eIF-2B, we have begun to clone, characterize, and express the corresponding cDNAs. We report here the cloning and characterization of a 1510-bp cDNA encoding the alpha subunit of eIF-2B from a rat brain cDNA library. The cDNA contains an open reading frame of 918 bp encoding a polypeptide of 305 aa with a predicted molecular mass of 33.7 kDa. This cDNA recognizes a single RNA species approximately 1.6 kb in length on Northern blots of RNA from rat liver. The predicted amino acid sequence contains regions identical to the sequences of peptides derived from bovine liver eIF-2B alpha subunit. Expression of this cDNA in vitro yields a peptide which comigrates with natural eIF-2B alpha in SDS/polyacrylamide gels. The predicted amino acid sequence exhibits 42% identity to that deduced for the Saccharomyces cerevisiae GCN3 protein, the smallest subunit of yeast eIF-2B. In addition, expression of the rat cDNA in yeast functionally complements a gcn3 deletion for the inability to induce histidine biosynthetic genes under the control of GCN4. These results strongly support the hypothesis that mammalian eIF-2 alpha and GCN3 are homologues. Southern blots indicate that the eIF-2B alpha cDNA also recognizes genomic DNA fragments from several other species, suggesting significant homology between the rat eIF-2B alpha gene and that from other species.