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An elongated form of T4 glutaredoxin with four extra residues.

Two different forms of T4 glutaredoxin (thioredoxin) arising from the same gene on a multicopy plasmid in an Escherichia coli expression system have been isolated and characterized. Up to one-fourth of purified T4 glutaredoxin has an extension of four amino acids in the carboxy terminus, with the sequence aspartate, arginine, isoleucine, lysine. This four-residue extension may be caused by a translational +1 frameshift at the UGA terminator codon.

Amino Acid Sequence↗

DNA sequence of the yeast transketolase gene.

Transketolase (EC 2.2.1.1) is the enzyme that, together with aldolase, forms a reversible link between the glycolytic and pentose phosphate pathways. We have cloned and sequenced the transketolase gene from yeast (Saccharomyces cerevisiae). This is the first transketolase gene of the pentose phosphate shunt to be sequenced from any source. The molecular mass of the proposed translated protein is 73,976 daltons, in good agreement with the observed molecular mass of about 75,000 daltons. The 5'-nontranslated region of the gene is similar to other yeast genes. There is no evidence of 5'-splice junctions or branch points in the sequence. The 3'-nontranslated region contains the polyadenylation signal (AATAAA), 80 base pairs downstream from the termination codon. A high degree of homology is found between yeast transketolase and dihydroxyacetone synthase (formaldehyde transketolase) from the yeast Hansenula polymorpha. The overall sequence identity between these two proteins is 37%, with four regions of much greater similarity. The regions from amino acid residues 98-131, 157-182, 410-433, and 474-489 have sequence identities of 74%, 66%, 83%, and 82%, respectively. One of these regions (157-182) includes a possible thiamin pyrophosphate (TPP) binding domain, and another (410-433) may contain the catalytic domain.

Aldehyde-Ketone Transferases↗

Cloning, nucleotide sequence, and chromosome localization of the human pleiotrophin gene.

Pleiotrophin (PTN), midkine (MK), and retinoic acid-induced heparin-binding (RI-HB) protein are members of a recently discovered family of developmentally regulated cytokines. We report here the cloning, sequencing, chromosomal localization, and structural organization of the genomic version of the human PTN gene and its comparison to the mouse MK gene. The PTN gene was found to be arranged in five exons and four introns, in a fashion similar to that of the mouse MK gene. Exon 1, as for MK, does not appear to encode amino acid sequence. As in the case of the MK gene, exon 2 encodes the hydrophobic leader sequence of PTN, which constitutes the beginning of gene translation. The signal peptide cleavage site of both genes lies toward the 3' end of exon 2. Exons 3 and 4 of PTN were most closely related to exons 3 and 4 of the MK gene; in particular, six of the ten cysteine residues were coded for in exon 3 and the remaining 4 in exon 4. The intron-exon splice junctions of both genes occurred through the same residues. The two genes were found to be less closely related in the fifth exon which encodes the highly basic C-terminal domains, the translation termination codon, and the polyadenylation signal of both cDNAs. We also report approximately 2000 bp of the 5' untranslated sequence of the PTN gene and the site of initiation of transcription in human placenta. PTN was localized to human chromosome 7q33-34 by fluorescence in situ hybridization. These data confirm the existence of a new gene family of developmentally regulated cytokines.

Amino Acid Sequence↗

Inhibition of human immunodeficiency virus type-1 env expression by C-5 propyne oligonucleotides specific for Rev-response element stem-loop V.

The binding of Rev to the Rev-response element (RRE) of the human immunodeficiency virus (HIV) is essential for RNA transport and expression of structural proteins such as gp160 encoded by env. To determine if env expression could be disrupted by complementary oligodeoxynucleotides (ODNs), band-shift studies were used to identify RRE sites that are essential for the formation of Rev-RRE complexes [Chin, D. J. (1992) J. Virol. 66, 600-607] or the stability of preformed complexes. In this report, we describe complete disruption of preformed Rev-RRE complexes by a subset of 15 ODNs complementary to stem-loop V. The most potent ODN complementary to bases CUGGGGCAUCAAGC disrupted 50% of preformed complexes at 1.2 microM, a 400-fold molar excess over the RNA. Expression of env in COS7 cells was blocked by nuclear microinjection of ODNs with C-5 propyne-modified pyrimidines and phosphorothioate linkages. Inhibition was highly dependent upon RNA target position, internucleotide chemistry, ODN sequence, and concentration. Unmodified phosphodiester or phosphorothioate ODNs were inactive. For the most potent ODN, 50% of the injected cells' env expression (I50) was blocked with 0.1 microM. A translational block is unlikely since these ODNs blocked expression of a luciferase vector in which the RRE was placed downstream of the termination codon. Consistent with their in vitro effects upon Rev-RRE complexes, stem-loop V ODNs were 9-fold more active than stem-loop II ODNs in blocking env expression while having a reduced (I50 = 0.27 microM) but equivalent potency against luciferase-RRE. These results suggest that disruption of Rev-RRE complexes may assist in blocking env expression.

Alkynes↗

Site-specific incorporation of nonnatural residues during in vitro protein biosynthesis with semisynthetic aminoacyl-tRNAs.

A method is presented for the incorporation of nonnatural amino acids into proteins during in vitro cell-free translation. A combination of chemical synthesis and run-off transcription was employed to prepare a semisynthetic, nonhypermodified tRNA(Gly) nonsense suppressor acylated with L-3-[125I]iodotyrosine. The presence of this synthetic tRNA during in vitro translation of mRNA containing a nonsense suppression site (e.g., a UAG termination codon) results in the incorporation of the nonnatural amino acid L-3-iodotyrosine into the polypeptide exclusively at the position corresponding to that site. Incorporation of the nonnatural amino acid L-3-[125I]iodotyrosine into the model polypeptide was assessed by quantitative and unambiguous determination of suppression efficiency, read-through, and site specificity of incorporation. Minor modifications of the method employed in this initial experiment also allow the rapid analysis of unlabeled acylated tRNA analogues. Under optimum conditions, the unlabeled amino acid L-3-iodotyrosine was found to be incorporated with a suppression efficiency of 65%. Other nonnatural residues, including N-methylphenylalanine, D-phenylalanine, and phenyllactic acid, were tested in the assay under these same conditions. Suppression efficiencies for this series ranged from 0 to 72% depending on the structure of the residue incorporated. Several other aspects of this methodology, such as tRNA structure and context effects, are briefly discussed.

Acylation↗

Characterization of a cDNA coding for human factor XII (Hageman factor).

Affinity-purified antibody against human factor XII (Hageman factor) has been radiolabeled with 125I and employed as a probe to screen a human liver cDNA expression library prepared in lambda gt11. Approximately 3.5 X 10(6) recombinant phages were screened for factor XII, and two positive clones were identified and plaque purified. The largest cDNA coding for factor XII was 1571 base pairs in length and coded for amino acid residues 127-596 in the mature protein, a termination codon of TGA, a 3' noncoding sequence of 147 nucleotides, and a poly(A) tail of 11 nucleotides. The second clone contained an insert of 1334 base pairs and coded for amino acid residues 200-596. The amino acid sequence predicted by the cDNAs was in excellent agreement with that previously determined by amino acid sequence analysis. The amino acid and DNA sequences in human factor XII showed considerable homology with the corresponding domains in other serine proteases, including prothrombin, plasminogen, tissue plasminogen activator, and urokinase.

Amino Acid Sequence↗

In vivo function of Escherichia coli pyruvate oxidase specifically requires a functional lipid binding site.

The pyruvate oxidase of Escherichia coli is a peripheral membrane flavoprotein that is dramatically activated by lipids. The enzyme strongly binds to phospholipid vesicles in vitro. In vivo, in addition to enzyme activation, binding is thought to be important to provide access of the enzyme to ubiquinone dissolved in the lipid bilayer. It was unclear if both or either of these attributes is needed for enzyme function in vivo. To differentiate between activation and lipid binding, we have constructed, using recombinant DNA techniques, a mutant gene that produces a truncated protein. The truncated protein lacks the last 24 amino acids of the C-terminus of the oxidase (due to introduction of a translation termination codon) and thus is closely analogous to the activated species produced in vitro by limited chymotrypsin cleavage [Recny, M.A., Grabau, C., Cronan, J.E., Jr., & Hager, L.P. (1985) J. Biol. Chem. 260, 14287-14291]. The truncated protein (like the protease-derived species) is fully active in vitro in the absence of lipid, and its activity is not further increased by addition of lipid activators. Moreover, the truncated enzyme fails to bind Triton X-114, a detergent that binds to and activates the wild-type oxidase. Strains producing the truncated protein were devoid of oxidase activity in vivo. This result indicates that binding to membrane lipids is specifically required for function of the oxidase in vivo; activation alone does not suffice.

Amino Acid Sequence↗

Isolation and characterization of a processed gene for human ceruloplasmin.

A processed pseudogene for human ceruloplasmin has been isolated that contains DNA corresponding to the functional gene sequence encoding the carboxy-terminal 563 amino acid residues and the 3' untranslated region. The pseudogene appears to have arisen from a processed RNA species, since intervening sequences coincident with those of the functional gene have been removed, with the exception of a short segment of intronic sequence which denotes the 5' boundary of the pseudogene. The nucleotide sequence of the pseudogene is highly homologous (97% sequence identity) with that of the wild-type gene, suggesting that pseudogene formation was a relatively recent evolutionary event. In addition to single base substitutions, there is a large 213 base pair (bp) deletion in the pseudogene sequence which corresponds to the location of an intron-exon junction in the functional gene. A 4 bp duplication that occurs at amino acid residue 683 of the wild-type coding sequence results in a frameshift mutation and introduces a premature translational termination codon at this point. This is concordant with the inability to detect a human liver transcript corresponding to the pseudogene by nuclease S1 mapping analysis. The 3' end of the pseudogene is characterized by a 62 bp segment composed mainly of repeated TC dinucleotides. On the basis of genomic Southern blot analysis performed under high-stringency conditions, the pseudogene that we have identified seems to comprise the only sequence in the human genome that is closely related to the wild-type gene. Using somatic cell hybridization, we have mapped the pseudogene to human chromosome 8.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Gene family of male-specific testosterone 16 alpha-hydroxylase (C-P-450(16) alpha) in mouse liver: cDNA sequences, neonatal imprinting, and reversible regulation by androgen.

The cDNA clone p16 alpha-1 for the male-specific isozyme (C-P-450(16) alpha)1 of testosterone 16 alpha-hydroxylase in livers of 129/J mice [Harada, N., & Negishi, M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 2024-2028] and two additional full-length cDNAs overlapping with p16 alpha-1 (p16 alpha-2 and p16 alpha-16) were sequenced. p16 alpha-2 contained a single open reading frame of 1512 nucleotides, consisting of 71 base pairs of the 5'-noncoding region and 63 base pairs of the 3'-noncoding region with an additional poly(A) tract. From this DNA sequence, C-P-450(16) alpha was deduced to contain 504 amino acids with a calculated molecular mass of 56,948 daltons. p16 alpha-1 showed a nucleotide sequence identical with that of p16 alpha-2 but lacked nine amino acid residues from the N-terminus. Another cDNA clone, p16 alpha-16, also exhibited the same coding sequence with the exception of a 142 base pair deletion spanning from nucleotide 853 to nucleotide 994 of p16 alpha-2. This deletion seems to be a whole exon of this gene, resulting in a shift of reading frame and an early termination codon at 10 amino acid residues from the deletion. The expected translation product of this mRNA is calculated to be 294 amino acids and 33,300 daltons. The putative poly(A) addition signal AATAAA is present for all three clones, but there are polymorphisms in the start sites of polyadenylation.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Mutations at the interdomain hinge region of the DadB alanine racemase: effects of length and conformational constraint of the linker sequence on catalytic efficiency.

The pentapeptide "hinge" region of the DadB alanine racemase links two structural domains of the protein [Galakatos, N. G., & Walsh, C. T. (1987) Biochemistry 26, 8475]. The presence of substrate markedly reduces the rate of hinge-specific proteolysis of this racemase and induces a conformational change observed by circular dichroism. To evaluate the possible contribution of the proteolytically sensitive hinge residues (-Y253GGGY257-) on catalytic efficiency, site-directed mutations were generated to probe the effects of size and conformational rigidity of that region. A bacterial overproducing system for the dadB gene was constructed that expresses the enzyme as 4.5% of total soluble protein. On this construct, a four-part ligation allowed the engineering of two unique and proximal restriction sites required for cassette mutagenesis at the hinge region. For two of the eight mutants generated, expressed protein could not be detected (deletion of -GGGY-; termination codon at position 255). Deletion of one or two of the three Gly residues had no effect on catalytic efficiency. Insertion of a fourth Gly resulted in a 5-fold drop in Vmax/Km. For G254P, G255P, and G256P, Vmax/Km was 60%, 126%, and 26% of the native enzyme, respectively. In all cases, the Km's remained essentially constant, suggesting that the hinge region is not involved in substrate binding. The rate of hinge-specific proteolysis of the mutants was faster than that of wild-type DadB except for the G255P protein for which it was equivalent.

Alanine Racemase↗

Organization of the human protein S genes.

Human genomic clones that span the entire protein S expressed gene (PS alpha) and the 3' two-thirds of the protein S pseudogene (PS beta) have been isolated and characterized. The PS alpha gene is greater than 80 kilobases in length and contains 14 introns and 15 exons, as well as 6 repetitive "Alu" sequences. Exons I and XV contain 112 and 1139 bp 5' and 3' noncoding segments in addition to the amino and carboxyl termini, respectively. Exons I-VIII encode protein segments that are homologous to the vitamin K dependent clotting proteins and are bounded by introns whose position and type are identical with other members of this protein family. Exons IX-XV encode protein segments homologous to sex hormone binding globulin (SHBG) and are bounded by introns of identical type and position as in the SHBG gene. Genomic clones for the PS beta gene cover a distance of greater than 55 kilobases and contain segments corresponding to amino acids 46-635 of the mature protein and the 1.1-kb 3' noncoding region of the cDNA. The presence of multiple base changes in the coding portions of this gene, resulting in termination codons and frame shifts, suggests that it is a pseudogene. Comparison of DNA sequences for the two genes reveals 97% identity for coding and 3' noncoding, and 95.4% for intronic regions, suggesting divergence of the two genes is a relatively recent event.

Amino Acid Sequence↗

Amino acid sequence of rat alpha-lactalbumin: a unique alpha-lactalbumin.

The amino acid sequence of rat alpha-lactalbumin has been determined. Unlike other alpha-lactalbumins which contain 122 or 123 amino acids, rat alpha-lactalbumin is unique in that it contains 140 amino acids. The extra amino acids are a 17 amino acid extension at the carboxyl terminus. The amino acid sequence of this extension is Gly124-Ala-Pro-Ala-Leu-Val-Val130-Pro-Ala-Leu-Asp-Gly135-Glu-Thr-Pro-Val-Pro140 . The extension is proline rich, which may contribute to the anomalous structural properties of rat alpha-lactalbumin. The amino acid sequence from residues 1 to 123 is similar to that of other alpha-lactalbumins. One possible explanation for the 17 amino acid extension is a mutation at the termination codon.

Amino Acid Sequence↗

Triphasic concentration effects of gentamicin on activity and misreading in protein synthesis.

Gentamicin is shown to exert a triphasic concentration effect on peptide synthesis in vitro with natural messengers. Low concentrations (up to 2 micron) caused slowing and a decrease in total synthesis, but little misreading (assayed with extracts lacking Glu-tRNA); the inhibition was greater with an initiating system (with phage RNA as messenger) than with pure chain elongation on purified endogenous polysomes of Escherichia coli. Moderate concentrations (up to 100 micron) slowed synthesis less, markedly increased its duration in the noninitiating system, and strongly stimulated misreading; at optimal concentrations total synthesis was even greater than normal. Moreover, with phage RNA these concentrations increased the synthesis of large polypeptides. We conclude that binding of gentamicin to its first site causes inhibition but little misreading; binding to additional site(s) partly reverses the inhibition by first-site binding and markedly stimulates misreading, and the misreading appears to favor "readthrough" of termination codons. In the third phase (greater than 100 micron) synthesis is slowed again but the pattern of misreading does not appear to be altered; this effect need not involve a specific further action on the ribosome.

Bacterial Proteins↗

Molecular characterization of a single mitochondria-associated double-stranded RNA in the green alga Bryopsis.

Mitochondria from the green alga Bryopsis sp. very often contained a 4.5 kb double-stranded RNA (dsRNA) at a defined level. Complementary DNA probes derived from the mitochondrial dsRNA hybridized with none of the algal chloroplast dsRNAs of 1.7 to 2.2 kb, but did hybridize with a similar-sized dsRNA among several dsRNAs from the mitochondria of B. maxima. Sequence analysis of the mitochondrial dsRNA from Bryopsis sp. revealed only two large, overlapping, open reading frames (ORFs) on one strand if UGA was taken as a non-termination codon, suggesting the independent phylogenetic evolution of the mitochondrial dsRNA. Consensus sequence for RNA-dependent RNA polymerase was found within the longer ORF (2472 bp) of the dsRNA. The overlapping 52 bp of the ORFs in different reading frames is suggestive of the occurrence of a -1 ribosomal frameshift in the mitochondrial translation system. The observed simple genetic structures suggest that the algal mitochondrial dsRNA might be deficient in a gene for movement from cell to cell in host plants and, hence, has a plasmid-like nature that is distinct from that of infectious plant viruses. The nature and origin of the endogenous dsRNAs of various sizes and their relationships are discussed.

Amino Acid Sequence↗

A cDNA clone to clover yellow vein potyvirus genome is highly infectious.

We obtained a highly infectious cDNA clone of clover yellow vein virus (CIYVV). The cDNA fragments, from which a full-length cDNA clone was constructed, were sequenced, and the complete nucleotide sequence of C1YVV RNA was determined. The viral genome is 9584 nucleotides (nt) in length excluding the poly(A) tail and contains one open reading frame (ORF) encoding a large polyprotein of 3072 amino acids. The non-coding region preceding the ORF is 190 nt long. The termination codon is followed by a 175-nt sequence. Seven potential protease NIa, one HC-pro and one P1 protease recognition sites were found in the C1YVV polyprotein by searching for cleavage consensus sequences among the potyvirus group. The cleavage dipeptides of C1YVV NIa protease are Q(E)/S(A,G). The F is conserved at the -2 position from the cleavage site except for at the P3/6K1 junction, and the V conserved at the -4 position among many potyviruses is not present at all. The genome organization of C1YVV was determined, and the amino acid sequence was compared with that of other potyviruses. The full-length cDNA clone of C1YVV was constructed by combining cDNA fragments and placed it under the control of the cauliflower mosaic virus 35S promoter. The full-length cDNA was constructed so that no extra nucleotide was present at the transcription initiation site and only 10 adenine residues were present at the 3' end of the C1YVV cDNA clone. Mechanical inoculation of a circular-formed plasmid DNA onto broad bean seedlings led to systemic infection, and the symptoms were similar to those caused by the wild-type virus but rather mild. Plasmid diluted as low as 500 pg/microl was able to induce symptoms, demonstrating that this full-length C1YVV cDNA is more infectious than any other infectious cDNAs so far reported. Filamentous particles reacting with the antiserum to C1YVV were observed in the crude sap of infected plants by immunoelectron microscopy, and genome replication was demonstrated by RT-PCR of 3' non-coding regions of C1YVV genome in total plant RNAs.

Amino Acid Sequence↗

Expression of the translational repressor NAT1 in experimental models of cardiac hypertrophy.

The development of hypertension-induced cardiac hypertrophy is a complex process involving a number of biochemical pathways. In particular, the translation initiation pathway has been postulated to play an important role in controlling cellular growth and proliferation in the cardiovascular system. Recently, a fundamental translational repressor, NAT1 (novel APOBEC target 1), has been identified. We have previously shown that NATI is developmentally-regulated in the heart of neonatal rats and its expression correlates with periods of rapid cardiac growth. The present investigation was designed to determine whether the expression of NAT1 is modified in the left ventricle of spontaneously hypertensive rats and 2-kidney-1-clip (2K1C) hypertensive rats. Northern blot analysis revealed an increase in NAT1 mRNA expression which correlates with the onset of cardiac hypertrophy. Unlike its pattern of mRNA expression, however, NAT1 protein level did not differ significantly from their respective controls throughout the time course. Interestingly, several protein species ranging in size from approximately 40-70 kDa were detected by Western blotting, in addition to the full length 97 kDa NAT1. Since the NAT1 transcript is a known substrate for the enzyme APOBEC-1 and possibly APOBEC-2, we speculate that these proteins may represent truncated fragments of NAT1 resulting from the formation of premature translation termination codons along the NAT1 transcript by APOBEC editing. Together, these results show that the ventricular expression of NAT1 is regulated at the transcriptional level during the early stages of genetic and 2K1C-induced hypertension and may be involved in the onset of left ventricular hypertrophy.

Acetyltransferases↗

Diagnosis of N-acetylglutamate synthase deficiency by use of cultured fibroblasts and avoidance of nonsense-mediated mRNA decay.

Molecular diagnosis of N-acetylglutamate synthase deficiency (NAGSD) has become possible now that the corresponding gene has been identified. We describe the genetic analysis of a patient with NAGSD using low-level transcripts derived from cultured fibroblasts. One defective allele (c.1306-1307insT) was detected by PCR amplification. However, the transcript from a second mutation (IVS3 - 2A>T), causing aberrant splicing with the generation of a premature termination codon, was not detected until interference of nonsense-mediated mRNA decay was abrogated by the translation inhibitor cycloheximide. We demonstrate that low-level transcripts in cells that do not express significant enzyme activity are a valuable tool for molecular studies of genetic alterations, and suggest routine abrogation of nonsense-mediated mRNA decay using cycloheximide when transcript analysis is performed.

Acetyltransferases↗

Fibrillin-1 (FBN1) gene frameshift mutations in Marfan patients: genotype-phenotype correlation.

Marfan syndrome (MFS) is a multisystemic disease associated with mutations in the fibrillin-1 gene. Most of the reported mutations are missense substitutions mainly affecting the epidermal growth factor (EGF)-like protein domain structure and the calcium-binding (cb) site. The aim of our study was to investigate the correlation between fibrillin-1 frameshift mutations and the clinical phenotype in patients affected by MFS. In 48 out of 66 Marfan patients a pathogenetic mutation was found. We detected novel mutations causing premature termination codon in exons 19, 37, 40 and 41 of four Italian patients. The first mutation in exon 19 (cbEGF #8 domain) results in a clinical phenotype involving mainly the skeletal and cardiovascular systems. Interestingly, we noticed that, while mutations in exons 37 and 41 (eight cysteine domains #4 and #5) are milder, the mutation in exon 40 (cbEGF #24 domain) is more severe and causes major cardiovascular involvement with thoracic and abdominal aortic aneurysms. It is noteworthy that the degree of the severity in the phenotype of one of our patients and another from the literature carrying a mutation in exon 41 could be explained with alterations in mRNA expression.

Adult↗