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PubMed2001

Characterization of a cDNA encoding a cathepsin L-like protein of Rhodnius prolixus.

The interaction of Rhodnius prolixus digestive enzymes with Trypanosoma cruzi could be important for parasite survival. We report herein the complete sequence of the messenger of a cathepsin L-like molecule (RpCat). The cDNA has 5'- and 3'- end UTRs and a methionine codon that corresponds likely to a translation initiation codon. In the deduced amino acid sequence, a region corresponding to an ERFININ domain, diagnostic of L-cathepsins, and a possible pro-peptide cleavage site were observed. At the C-terminus, a nine-amino acid sequence, almost identical to a secretion signal of human cathepsin L was found. RpCat messenger was expressed in intestines of R. prolixus adults, and from 1st to 4th but not in 5th instar nymph stages. In a similarity analysis, RpCat was grouped with L cathepsins forming a clear group separate of the B cathepsins.

3' Untranslated Regions↗

PubMed1986

Human delta-aminolevulinate dehydratase: nucleotide sequence of a full-length cDNA clone.

Two cDNAs encoding human delta-aminolevulinate dehydratase (ALA-D; porphobilinogen synthase; EC 4.2.1.24), the second enzyme in the heme biosynthetic pathway, were identified, recloned into bacteriophage M13, and sequenced by primer extension. The first clone with an 827-base-pair (bp) pEX-ALA-D cDNA insert, shown to contain DNA sequences that were colinear with four bovine ALA-D peptide sequences, was used to screen a pKT218 human liver library. A second clone containing a 1200-bp insert was identified that contained an open reading frame of 990 bp as well as 5' (66 bp)- and 3' (94 bp)-untranslated regions, the latter terminating in poly(dA). The predicted N-terminal amino acid sequence was colinear with the first 13 residues of microsequenced ALA-D purified from human erythrocytes. The ATG initiation codon was preceded by ACGCC, a functional initiation sequence, while an upstream (position -32), in-phase AACTG ATG sequence was entirely nonhomologous with the initiation consensus sequence and, therefore, presumed to be nonfunctional. The unusual polyadenylylation signal, AGTAAA, has been reported only in the human HRAS1 gene. The nucleotide sequences of the two cDNA clones differed at position 730 or 733 and encoded two differently charged amino acids. This nucleotide difference may be the basis for the polymorphic charge isozymes of human ALA-D. The sequence encoding this zinc metalloenzyme contained a cysteine- and histidine-rich binding site for zinc and an unusual region of charge complementarity surrounding the active lysine residue in the catalytic site.

Amino Acid Sequence↗

PubMed1992

Mutation creates an open reading frame within the 5' untranslated region of macaque erythrocyte carbonic anhydrase (CA) I mRNA that suppresses CA I expression and supports the scanning model for translation.

A variant allele at the CA I locus that produces a deficiency of erythrocyte-specific CA I occurs as a widespread polymorphism in pigtail macaques from southeast Asia. Sequence analyses revealed a C----G substitution 12 nucleotides downstream of the cap site in the variant erythrocyte CA I mRNA. This mutation forms a new AUG start site and an open reading frame coding for 26 amino acids that terminates 6 nucleotides before the normal AUG initiation codon for CA I. It appears that the presence of this upstream open reading frame greatly diminishes reinitiation of translation from the normal start site, resulting in trace levels of CA I in erythrocytes. Preferential use of the first AUG codon supports the scanning model for translation initiation in eukaryotes.

Animals↗

PubMed1987

Direct expression of a synthetic somatomedin C gene in Escherichia coli by use of a two-cistron system.

Direct expression of a growth-promoting peptide hormone, somatomedin C/insulin-like growth factor I, which is quite difficult due to the instability of somatomedin C itself in Escherichia coli, has been achieved by the use of a two-cistron system. Assuming that basic somatomedin C might be stabilized by forming a complex with an acidic polypeptide, we constructed synthetic genes consisting of two cistrons; an acidic 93-amino-acid polypeptide was coded in the first cistron followed by a synthetic somatomedin C gene in the second cistron. The chain termination codon for the first polypeptide overlapped the initiation codon for the second polypeptide in the intercistronic region, as occurs in the polycistronic E. coli tryptophan operon, whose products are associated in multi-subunit enzyme complexes. In the expression of the resulting genetic system, recombinant somatomedin C associated with the acidic polypeptide was accumulated to high levels in the cells. After treatment of the product with acetic acid to dissociate the two components, the recombinant somatomedin C was isolated in a yield of 4.0 mg from a liter of culture broth at A600 = 1.6. It was determined to be Met-somatomedin C by chymotryptic mapping as well as amino-terminal analysis.

Amino Acid Sequence↗

PubMed1991

Analysis of the lacZ sequences from two Streptococcus thermophilus strains: comparison with the Escherichia coli and Lactobacillus bulgaricus beta-galactosidase sequences.

The lacZ gene from Streptococcus thermophilus A054, a commercial yogurt strain, was cloned on a 7.2 kb PstI fragment in Escherichia coli and compared with the previously cloned lacZ gene from S. thermophilus ATCC 19258. Using the dideoxy chain termination method, the DNA sequences of both lacZ structural genes were determined and found to be 3071 bp in length. When the two sequences were more closely analysed, 21 nucleotide differences were detected, of which only nine resulted in amino acid changes in the proteins, the remainder occurring in wobble positions of the respective codons. Only three bases separated the termination codon for the lacS gene from the initiation codon for lacZ, suggesting that the lactose utilization genes are organized as an operon. The amino acid sequence of the beta-galactosidase, derived from the DNA sequence, corresponds to a protein with a molecular mass of 116860 Da. Comparison of the S. thermophilus amino acid sequences with those from Lactobacillus bulgaricus, E. coli and Klebsiella pneumoniae showed 48, 35 and 32.5% identity respectively. Although little sequence homology was observed at the DNA level, many regions conserved in the amino acid sequence were identified when the beta-galactosidase proteins from S. thermophilus, E. coli and L. bulgaricus were compared.

Amino Acid Sequence↗

PubMed1985

Attachment of the 5'-terminal portion of globin mRNAs to 5S-RNA X L5-protein in the 80S initiation complex.

An 80S initiation complex was formed by incubating a heterologous cell-free system with 125I-labeled globin mRNAs in the presence of sparsomycin. The 80S initiation complex was then digested with micrococcal nuclease. The ribosomal 5S-RNA X L5-protein (5S RNP) fraction, released by EDTA treatment, contained 125I-labeled mRNA fragments. The attachment of labeled mRNA fragments to 5S RNP was shown by (a) CsCl isopycnic centrifugation, (b) recentrifugation through a sucrose density gradient and (c) acrylamide gel electrophoresis of 5S RNP purified by (b). Labeled fragments were released from 5S RNP by treatment with sodium dodecyl sulfate or pronase, indicating the participation of protein L5 in the attachment. The attached mRNA fragments were 23-25 nucleotides in length. Hybridization experiments, using restriction fragments of cDNA for rabbit beta globin mRNA, showed that the attached mRNA fragments were derived from the 5' portion of globin mRNAs. The attachment of 125I-labeled mRNA fragments to 5S RNP was also observed in the 80S initiation complex formed by incubation of reticulocyte lysate with 125I-labeled globin mRNA, but not in labeled polysomal fractions. These findings may indicate that 5S RNP interacted with the 5' portion of globin mRNA, containing the translation initiation codon of globin mRNA in the 80S initiation complex. The biochemical significance of these results is discussed.

Animals↗

PubMed1987

A new human species of aldolase A mRNA from fibroblasts.

A full-length cDNA aldolase A clone was isolated from a human fibroblast cDNA library and completely sequenced. Excluding the poly(A) tail, the clone covers 1095 base pairs (bp) of the coding region, plus 199 bp downstream for the termination codon and 146 bp upstream for the initiation codon, within a total of 1440 bp. Primer extension experiments performed with human cultured fibroblast mRNA indicate an elongated product of a further 40 bp. These results evaluated together with those obtained in a concurrent study concerning aldolase A mRNA isolated from human liver are direct evidence of aldolase A mRNA multiplicity in man. The data also suggest the existence in mammals of three different classes of aldolase A mRNA, which would account for tissue specificity and resurgence of foetal expression in tumors.

Amino Acid Sequence↗

PubMed1994

Molecular cloning and sequence analysis of the proBA operon from an extremely thermophilic eubacterium Thermus thermophilus.

A 3.6 kb DNA fragment carrying the Thermus thermophilus proBA region, which encodes the first two steps in the proline biosynthetic pathway, was cloned from the Thermus thermophilus gene library, and its complete nucleotide sequence was determined. The deduced amino acid sequence of gamma-glutamyl kinase (40,657 Da), the product of proB gene, and gamma-glutamyl phosphate reductase (48,747 Da), the product of proA gene, showed 44.1% and 44.4% identity to those of Escherichia coli, respectively. The termination codon of the proB gene and the initiation codon of the proA gene overlapped by 2 bp. A possible transcriptional termination structure was found downstream of the proA gene but not downstream of the proB gene. These results indicate that the proBA genes of T. thermophilus form a single operon as in E. coli.

Aldehyde Oxidoreductases↗

PubMed1987

Sequence analysis of the Escherichia coli dnaE gene.

We have determined the sequence of a 4,350-nucleotide region of the Escherichia coli chromosome that contains dnaE, the structural gene for the alpha subunit of DNA polymerase III holoenzyme. The dnaE gene appeared to be part of an operon containing at least three other genes: 5'-lpxB-ORF23-dnaE-ORF37-3' (ORF, open reading frame). The lpxB gene encodes lipid A disaccharide synthase, an enzyme essential for cell growth and division (M. Nishijima, C.E. Bulawa, and C.R.H. Raetz, J. Bacteriol. 145:113-121, 1981). The termination codons of lpxB and ORF23 overlapped the initiation codons of ORF23 and dnaE, respectively, suggesting translational coupling. No rho-independent transcription termination sequences were observed. A potential internal transcriptional promoter was found preceding dnaE. Deletion of the -35 region of this promoter abolished dnaE expression in plasmids lacking additional upstream sequences. From the deduced amino acid sequence, alpha had a molecular weight of 129,920 and an isoelectric point of 4.93 for the denatured protein. ORF23 encoded a more basic protein (pI 7.11) with a molecular weight of 23,228. In the accompanying paper (D.N. Crowell, W.S. Reznikoff, and C.R.H. Raetz, J. Bacteriol. 169:5727-5734, 1987), the sequence of the upstream region that contains lpxA and lpxB is reported.

Amino Acid Sequence↗

PubMed1987

Improved mammalian vectors for high expression of G418 resistance.

Cell lines, such as those of teratocarcinoma and embryonic stem cells, fail to support high G418 resistance after transfection of neo vectors. To alleviate this, we modified pSV2-neo in two steps, first with tandem promoters of SV40 early genes and HSVtk, then by removing an improper met codon located immediately upstream of the authentic initiator codon in the mRNA sequence. In the final product, pSTneoB, the neo transcription unit has XhoI sites at both ends. pSTneoB yields G418-resistant transformants of teratocarcinoma cells at dramatically higher efficiencies than pSV2-neo. This vector extends the application of G418 selection in gene transfer to a wider range of cell types.

Animals↗

PubMed2004

Genome sequencing and annotation: an overview.

Many microbial genome sequences have been determined, and more new genome projects are ongoing. Shotgun sequencing of randomly cloned short pieces of genomic DNA can provide a simple way of determining whole genome sequences. This process requires sequencing of many fragments, compilation of the separate sequences into one contiguous sequence, and careful editing of the assembled sequence. The genes present on the microbial genome are then predicted using clues derived from typical gene features, such as codon usage, ribosomal binding sequences, and bacterial initiation codons. Function of genes is predicted by homology searches performed against either public or well-established protein databases. This chapter discusses each of these stages in a genome-sequencing project.

Amino Acid Sequence↗

PubMed1990

Cascade of overlapping late genes in bacteriophage T4.

The DNA sequences of genes 9, 10, 11, 12, and wac, which encode the structural proteins in the bacteriophage T4 base plate, were determined. These genes form a single operon which is transcribed in a clockwise direction from a single late promoter in the TATAAATA region located upstream of gene 9 at position -10. A feature of the operon is an overlap between the termination codon of each upstream gene and the initiation codon of its downstream gene. With the exception of gene 10, the open reading frames encode proteins which have a calculated molecular mass close to that obtained experimentally. The reading frame of gene 10 encodes a polypeptide with a calculated molecular mass of 66.2 kDa, which is at least 22 kDa less than that in the phage particle. Thus the mature protein encoded by gene 10 is possibly a product of the fusion of two adjacent phage genes. The hybrid protein may be formed by a frameshift during the translation of messenger RNA at the end of gene 9 or gene 10.

Amino Acid Sequence↗

PubMed1985

Translational coupling at the intercistronic boundary of an artificially constructed operon in Escherichia coli.

By using recombinant DNA techniques an artificial operon was constructed that codes for two fusion proteins under the control of the beta-lactamase promoter of plasmid pBR322. The two proteins are: 1. beta-lactamase-trp B (43 kd) 2. trpA-beta-galactosidase (120 kd). Frameshift mutations in the N-terminal region of the first gene resulted in a dramatic reduction in the synthesis of the protein coded by the second gene. This strong polar effect could not be accounted for by correspondingly lower level of the distal region of the messenger RNA, only by "translational coupling" due to the overlap of the termination codon of the first gene with the initiation codon of the second gene. It was concluded that the strong "translational coupling" observed in this artificial operon can be generally used to ensure coordinated high-level synthesis of proteins in operons constructed by recombinant DNA techniques.

DNA, Recombinant↗

PubMed1983

High-level expression of oncogenes in Escherichia coli.

A plasmid, pJL6, was constructed that contains a unique Cla I site 12 codons beyond the bacteriophage lambda cII gene initiation codon, as well as an adjacent unique Hind III site. These sites allowed us to fuse the sequences from the avian myelocytomatosis virus (MC29) v-myc gene, the avian myeloblastosis virus (AMV) v-myb gene, and the Harvey murine sarcoma virus (Ha-MuSV) v-ras gene to the amino-terminal portion of the cII gene. Transcription of the hybrid genes is controlled from the lambda PL promoter. When this promoter is derepressed, E. coli cells harboring the chimeric plasmid produce levels of fusion proteins that amount to over 5% of total cellular protein. Antibodies raised by the cII-myc fusion protein form an immunoprecipitate with the MC29 gene product, P110gag-myc. The cII-ras fusion protein is precipitated by monoclonal antibodies directed toward the Ha-MSV p21ras, binds GDP, and is capable of autophosphorylation.

Amino Acid Sequence↗

PubMed1983

Nucleotide sequence analysis of the A2 and B subunits of Vibrio cholerae enterotoxin.

We have determined the sequence of the DNA encoding the A2 (gamma) and B subunits of Vibrio cholerae enterotoxin. The order of the subunits as they would be transcribed is A2-B and the termination codon of the A2 subunit overlaps the initiation codon of the B subunit by four bases. Sequence analysis revealed a region capable of coding for a 21-amino acid leader peptide located at the NH2 terminus of the B subunit. While the nucleotide sequence homology between the cholera enterotoxin subunits and the analogous sequences of the genes for Escherichia coli heat-labile enterotoxin (LT) was 72 and 77% for the A2 and B subunits, respectively, the predicted amino acid sequences of the A2 subunits were less similar. Twenty-nine of 46 (63%) amino acids of the A2 subunits and 98 of 124 (79%) amino acids of the B subunits were identical between cholera enterotoxin and LT. The predicted amino acid sequence of the enterotoxin from a V. cholerae El Tor biotype strain reported here differs from the previously published amino acid sequences of the toxin from a classical biotype of V. cholerae at seven residues. Comparison of the A2 and B amino acid sequences among El Tor and classical biotypes of V. cholerae and E. coli LT demonstrates two regions of highly conserved sequences: 12 and 22 uninterrupted amino acids are the same among the A2 and B subunits, respectively, from the three strains.

Amino Acid Sequence↗

PubMed2004

Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs.

It is generally accepted that translation in bacteria is initiated by 30S ribosomal subunits. In contrast, several lines of rather indirect in vitro evidence suggest that 70S monosomes are capable of initiating translation of leaderless mRNAs, starting with the A of the initiation codon. In this study, we demonstrate the proficiency of dedicated 70S ribosomes in in vitro translation of leaderless mRNAs. In support, we show that a natural leaderless mRNA can be translated with crosslinked 70S wild-type ribosomes. Moreover, we report that leaderless mRNA translation continues under conditions where the prevalence of 70S ribosomes is created in vivo, and where translation of bulk mRNA ceases. These studies provide in vivo as well as direct in vitro evidence for a 70S initiation pathway of a naturally occurring leaderless mRNA, and are discussed in light of their significance for bacterial growth under adverse conditions and their evolutionary implications for translation.

5' Untranslated Regions↗

PubMed1988

Synthesis of adeno-associated virus structural proteins requires both alternative mRNA splicing and alternative initiations from a single transcript.

The three adeno-associated virus type 2 (AAV2) structural proteins (A, B, and C) are specified by transcripts generated from the most-rightward promoter (p40). Protein C (60 kilodaltons [kDa]), the most abundantly produced, is entirely contained within B (72 kDa) which, in turn, is contained within A (90 kDa). Although neither of the known structures of p40 transcripts, an unspliced 2.6-kilobase (kb) RNA and a spliced 2.3-kb RNA, possesses an AUG-initiated open reading frame that accounts for the synthesis of proteins A and B, recent evidence indicates that B is initiated by a unique eucaryotic initiation codon (ACG) (S.P. Becerra, J.A. Rose, M. Hardy, B. Baroudy, and C.W. Anderson, Proc. Natl. Acad. Sci. USA 82:7919-7923, 1985). In the present study, we analyzed the in vitro translation of AAV capsid proteins from synthetic transcripts and the in vivo expression of AAV mRNA and capsid proteins in 293 cells transfected with AAV DNA constructs. The results demonstrated that AAV transcripts contain only one functional 5' splice donor site, that synthesis of capsid proteins from the unspliced 2.6-kb transcript is very inefficient, that transcripts without the intervening sequence (IVS) (i.e., the 2.3-kb RNA) do not produce protein A but effectively synthesize proteins B and C, and that protein A is actively synthesized from transcripts which contain the last 34 bases of the IVS. Protein A initiates within this 34-base segment in reading frame 1, apparently with the AUG codon at nucleotide 2203, and then elongates into the B and C open reading frame. Because A is inefficiently synthesized from the 2.6-kb transcript, we conclude that an effective A transcript is generated by alternative splicing and that the alternative 3' acceptor site may lie at nucleotide 2200 within a context of...CAG]GTA. The levels of B and C produced by a synthetic transcript devoid of the IVS suggest that the known 2.3-kb RNA is the main source of these proteins and indicate that this single RNA species expresses both proteins by alternative use of their respective initiation codons.

Capsid↗

PubMed1981

Factors governing the expression of a bacterial gene in mammalian cells.

Cultured monkey kidney cells transfected with simian virus 40 (SV40)-pBR322-derived deoxyribonucleic acid (DNA) vectors containing the Escherichia coli gene (Ecogpt, or gpt) coding for the enzyme xanthine-guanine phosphoribosyltransferase (XGPRT) synthesize the bacterial enzyme. This paper describes the structure of the messenger ribonucleic acids (mRNA's) formed during the expression of gpt and an unexpected feature of the nucleotide sequence in the gpt DNA segment. Analyses of the gpt-specific mRNA's produced during infection of CV1 cells indicate that in addition to the mRNA's expected on the basis of known simian virus 40 RNA splicing patterns, there is a novel SV40-gpt hybrid mRNA. The novel mRNA contains an SV40 leader segment spliced to RNA sequences transcribed from the bacterial DNA segment. The sequence of the 5'-proximal 345 nucleotides of the gpt DNA segment indicates that the only open translation phase begins with an AUG about 200 nucleotides from the end of the gpt DNA. Two additional AUGs as well as translation terminator codons in all three phases precede the XGPRT initiator codon. Deletion of the two that are upstream of the putative start codon increases the level of XGPRT production in transfected cells; deletion of sequences that contain the proposed XGPRT initiator AUG abolishes enzyme production. Based on the location of the XGPRT coding sequence in the recombinants and the structure of the mRNA's, we infer that the bacterial enzyme can be translated from an initiator AUG that is 400 to 800 nucleotides from the 5' terminus of the mRNA and preceded by two to six AUG triplets.

Animals↗