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Both forms of translational initiation factor IF2 (alpha and beta) are required for maximal growth of Escherichia coli. Evidence for two translational initiation codons for IF2 beta.

The gene infB codes for two forms of translational initiation factor IF2; IF2 alpha (97,300 Da) and IF2 beta (79,700 Da). IF2 beta arises from an independent translational event on a GUG codon located 471 bases downstream from IF2 alpha start codon. By site-directed mutagenesis we constructed six different mutations of this GUG codon. In all cases, IF2 beta synthesis was variably affected by the mutations but not abolished. We show that the residual expression of IF2 beta results from translational initiation on an AUG codon located 21 bases downstream from the mutated GUG. Furthermore, two forms of IF2 beta have been separated by fast protein liquid chromatography and the determination of their N-terminal sequences indicated that they resulted from two internal initiation events, one occurring on the previously identified GUG start codon, the other on the AUG codon immediately downstream. We conclude that two forms of IF2 beta exist in the cell, which differ by seven aminoacid residues at their N terminus. Only by mutating both IF2 beta start codons could we construct plasmids that express only IF2 alpha. A plasmid expressing only IF2 beta was obtained by deletion of the proximal region of the infB gene. Using a strain that carries a null mutation in the chromosomal copy of infB and a functional copy of the same gene on a thermosensitive lysogenic lambda phage, we could cure the lambda phage when the plasmids expressing only one form of IF2 were supplied in trans. We found that each one of the two forms of IF2, at near physiological levels, can support growth of Escherichia coli, but that growth is retarded at 37 degrees C. This result shows that both forms of IF2 are required for maximal growth of the cell and suggests that they have acquired some specialized but not essential function.

Amino Acid Sequence

Transient expression of deletion mutants of the herpes simplex virus thymidine kinase-encoding gene in mouse fibroblast cells.

Previous studies have shown that at least three polypeptides of 43, 39 and 38 kDa are translated from separate AUG codons of the thymidine kinase (TK) encoding mRNA of herpes simplex virus type 1. In addition, small tk-specific transcripts initiated within the tk coding region were observed. However, functional activity of these three proteins and their role in establishing of the TK+ cell phenotype is not yet clear. In order to locate the 5' boundary of the gene encoding functionally active TK, we constructed a set of deletion mutants with truncated 5' ends and examined their ability to provide a TK+ phenotype after microinjection into nuclei of LTK- cells. The results demonstrate that nucleotide sequences upstream from the second ATG codon can be removed without affecting the TK+ phenotype. Deletion of the second start codon and its downstream region inactivates the TK function. Those deletion mutants which contain only the third ATG codon are TK-. Thus, the 38-kDa polypeptide that initiates at the third start codon is not endowed with the TK+ activity. Constructs containing deletions up to nt +210 and lacking all 5'-end canonical and aberrant transcription control regions, as well as first start codon, can provide the TK+ function.

Animals

Analysis of GPT activity in mammalian cells with a chromosomally integrated shuttle vector containing altered gpt genes.

The molecular mechanisms of reversion in mammalian cells were studied utilizing the pZipGptNeo shuttle vector, with the bacterial gpt gene in the vector integrated into the chromosomal DNA of mouse cells. From mutant cell lines containing gpt genes with single base changes, revertants were selected for the reappearance of GPT activity. The copy number and expression of the gpt genes in such revertants were analyzed, and the GPT activity encoded by revertant genes in both mammalian cells and bacteria characterized. Revertants with wild-type amino acid sequence had, on average, the highest levels of GPT activity. Revertants with amino acid sequences different from the original mutants but not corresponding to wild-type had, on average, approximately half the level of GPT activity as wild-type revertants. Revertants that still contained the original mutation in the gpt gene had even lower levels of activity. These revertants were found to have amplified mutant gpt genes, which, when transferred into bacteria, were seen to encode for GPT polypeptides with partial enzymatic activity. A revertant in which the original mutation that destroyed the AUG translational start codon was retained but in which there was a secondary mutation upstream of the start codon also was characterized. The second mutation generated an in-frame CUG codon that apparently functioned as an alternative, upstream translational start codon.

Animals

Modification in framework region I results in a decreased affinity of chimeric anti-TAG72 antibody.

A mouse/human chimeric B72.3P-1-6 antibody was produced by construction of a novel expression vector mpSV2neo-EP2-V-Crl containing the same gene fragments as the expression vector mpSV2neo-EP1-V-Crl (Xiang J., Roder J. and Hozunni N., submitted to Molec. Immun., 1991) except the promoter (P2) fragment in which the translation start codon ATG is retained. The expression vector was transfected into a heavy chain loss mutant cell line, B72.3M1. The translation of the chimeric heavy chain may start at the exogenous start codon ATG within the P2 fragment, which is 27 base pairs upstream of the endogenous start codon ATG in B72.3 heavy chain V region cDNA fragment, leading to an alteration in leader sequence cleavage sites and the formation of chimeric heavy chain with an elongation in the FR1 region. Chimeric B72.3P-1-6 antibody retained binding specificity to TAG72 antigen, but showed an eight-fold decrease in binding affinity to TAG72 compared with chimeric B72.3-1-3 antibody. This suggests that residues in FRI contribute to the correct folding of the antibody binding region of the B72.3 antibody.

Amino Acid Sequence

Transcriptional analysis of the isopenicillin N synthase-encoding gene of Streptomyces clavuligerus.

The gene (pcbC) encoding isopenicillin N synthase of Streptomyces clavuligerus is separated from an upstream open reading frame (ORF) by a 31-bp intergenic region. Inspection of the sequence of this intergenic region did not identify a promoter sequence. The promoter probe plasmid, pIJ4083, which contains the promoter-less catechol-2,3-dioxygenase (C23O)-encoding gene (xylE) as a reporter gene, was used to analyze the sequence upstream from the pcbC gene for promoter activity. Introduction of an SphI site at the start codon of pcbC by site-directed mutagenesis allowed the cloning of a 335-bp fragment (-334 to +1 in relation to the pcbC start codon) immediately upstream from xylE in pIJ4083. C23O activity was detected in both Streptomyces lividans and S. clavuligerus cultures that contained the upstream fragment, suggesting the presence of a promoter sequence. Northern analysis of total RNA extracted from S. clavuligerus identified a monocistronic 1.2-kb transcript hybridizing to a pcbC-specific probe. When RNA was isolated at various times during growth in liquid culture, the presence of a transcript was first detected during stationary phase. Analysis of the pcbC transcript by primer extension located the transcription start point to a C residue within the upstream ORF, 91 bp upstream from the pcbC start codon.

Blotting, Northern

In vivo translational start site selection on leaderless mRNA transcribed from the Streptomyces fradiae aph gene.

The message of the Streptomyces fradiae aph gene lacks a leader sequence and therefore is translated in the absence of a conventional Shine-Dalgarno interaction between mRNA and 30S ribosomal subunits. Insertion mutations generating short leaders of 2 or 4 nucleotides on the 5' end of the aph transcript reduced translational efficiency. A 4-base leader (5'-AUGC-3') placing a potential out-of-frame start codon immediately upstream of the aph coding sequence prevented detectable translation in the aph reading frame. The upstream AUG in this mutant was able to drive the expression of a reporter gene in a translational fusion vector, implying that this start codon was utilized in favor of the downstream AUG. Additional leaders (5'-AUAUGC-3' or 5'-CAUAUGC-3') placing 2 or 3 nucleotides 5' to the upstream AUG relieved this apparent discrimination, permitting translation of the APH protein from the downstream AUG. These results suggest that the position of a start codon with respect to the 5' terminus of aph mRNA is a determinant of translational efficiency and start site selection.

Base Sequence

Construction and characterization of an Escherichia coli mutant with a deletion of the metZ gene encoding tRNA (f1Met).

The Escherichia coli metZ gene encoding tRNA (f1Met) was replaced by the chloramphenicol-resistance-encoding gene. The resulting mutant exhibited slightly lower growth rates as compared to the wild type at 37 degrees C or 42 degrees C, but grew apparently slower than the latter at 30 degrees C, indicating a slight cold sensitivity of growth. beta-Galactosidase was produced efficiently from the start codon AUG of the intact lacZ gene or trpA'::lac' Z fusion gene, in the metZ deletion mutant. The lac repressor from the lacI gene and the chimeric protein from a hupB' ::lac'Z fusion gene, whose start codons are GUG, were also synthesised in the deletion mutant. These results provide evidence that tRNA (f1Met) is not essential for growth of E. coli and that the start codons, AUG and GUG, are both recognized by tRNA (f1Met), a minor N-formyl methionine-specific tRNA, in the tRNA (f1Met)-depleted cells.

Blotting, Southern

Construction and characterization of an Escherichia coli mutant deficient in the metY gene encoding tRNA(f2Met): either tRNA(f1Met) or tRNA(f2Met) is required for cell growth.

The Escherichia coli metY gene, encoding tRNA(f2Met), was split by the kanamycin-resistance-encoding gene. The resulting mutant exhibited the same growth rate as the wild type, indicating that tRNA(f2Met) is not indispensable as is the case with the metZ gene encoding tRNA(f1Met) [Kenri et al., Gene 103 (191) 31-36]. beta-Galactosidase was produced efficiently from the start codon AUG of the intact lacZ gene or a trpA'::lac'Z fusion gene, in the metY mutant. The lac repressor from the lacI gene and the chimeric protein from a hupB'::lac'Z fusion gene, whose start codons are GUG, were also synthesized efficiently in the insertion mutant. These results provide evidence that tRNA(f2Met) is not essential for growth of E. coli and that the start codons, AUG and GUG, are both recognized by tRNA(f1Met), a major N-formyl methionine-specific tRNA, in the tRNA(f2Met)-depleted cells. We were unable to construct mutants deficient in both tRNA(f1Met) and tRNA(f2Met) by P1 phage-mediated transduction with the metY and metZ mutations. Moreover, the ampicillin-resistance marker of the pUC9 plasmid carrying metZ+ was not cured at 42 degrees C in host cells with the polAts and metY-metZ double mutations. These results indicate that either tRNA(f1Met) or tRNA(f2Met) is required for the growth of E. coli.

Blotting, Southern

Broad-host-range properties of plasmid RK2: importance of overlapping genes encoding the plasmid replication initiation protein TrfA.

The trfA gene, encoding the essential replication initiation protein of the broad-host-range plasmid RK2, possesses an in-frame overlapping arrangement. This results in the production of TrfA proteins of 33 and 44 kDa, respectively. Utilizing deletion and site-specific mutagenesis to alter the trfA operon, we compared the replication of an RK2-origin plasmid in several distantly related gram-negative bacteria when supported by both TrfA-44 and TrfA-33, TrfA-33 alone, or TrfA-44/98L (a mutant form of the TrfA-44 protein) alone. TrfA-44/98L is identical to wild-type TrfA-44 with the exception of a single conservative amino acid alteration from methionine to leucine at codon 98; this alteration removes the translational start codon for the TrfA-33 protein. Copy number and stability were virtually identical for plasmids containing both TrfA-44 and TrfA-33 proteins or TrfA-44/98L alone in Pseudomonas aeruginosa and Agrobacterium tumefaciens, two unrelated bacteria in which TrfA-33 is poorly functional. This, along with recent in vitro studies comparing TrfA-44, TrfA-33, and TrfA-44/98L, suggests that the functional activity of TrfA-44 is not significantly affected by the 98L mutation. Analysis of minimal RK2 derivatives in certain gram-negative bacterial hosts suggests a role of the overlapping arrangement of trfA in facilitating the broad host range of RK2. RK2 derivatives encoding TrfA-44/98L alone demonstrated decreased copy number and stability in Escherichia coli and Azotobacter vinelandii when compared with derivatives specifying both TrfA-44 and TrfA-33. A strategy employing the trfA-44/98L mutant gene and in vivo homologous recombination was used to eliminate the internal translational start codon of trfA in the intact RK2 plasmid. The mutant intact RK2 plasmid produced only TrfA-44/98L. A small reduction in copy number and beta-lactamase expression resulted in E. coli, suggesting that overlapping trfA genes also enhance the efficiency of replication of the intact RK2 plasmid.

Amino Acid Sequence

Expression of a downstream gene from a bicistronic transcription unit in transgenic tobacco plants.

We have constructed a set of plasmids carrying an artificial compact stop-start codon sequence, TGATGTAACATGA, between an upstream open reading frame, terminating at one of the stop codons, and a downstream kanamycin-resistance (KmR)-encoding gene (nptII) initiating at the second ATG. These plasmids were introduced into tobacco protoplasts by direct gene transfer. The efficiency of expression of the downstream nptII gene was measured by scoring the number of KmR transformants. With a closer distance between the functional stop and start codons, a tendency to less efficient expression of nptII was found. The integration and expression of both genes as a bicistronic transcription unit were verified by Southern- and Northern-blot analyses. A possible application of the compact stop-start codon sequence for insertional mutagenesis is discussed.

Base Sequence

Analysis of barley nitrate reductase cDNA and genomic clones.

Barley nitrate reductase cDNA and genomic clones were isolated by homology with the barley nitrate reductase cDNA clone bNRp10 and sequenced. This is the first reported analysis of a full-length nitrate reductase gene and its corresponding cDNA in the same species. The longest cDNA clone extends to within 9 bp of the ATG start codon and the sequence is similar to that reported for the higher plant NR sequences. As expected, the amino acid sequence of barley nitrate reductase is more related closely to the rice (84% homology) than to the Arabidopsis (62%) sequence. Four different polyA addition sites were identified from sequence analysis of nine barley NR cDNA clones. A 7.3 kb region of a genomic recombinant lambda clone was subcloned as two contiguous BamHI fragments into p Bluescript, designated pMJ7 and pMJ8, and sequenced. These clones include the entire nitrate reductase coding region, one large intron, 2.7 kb of untranslated sequence 5' to the translation start codon and 0.25 kb 3' to the translation termination codon. The mRNA cap site was identified as a cytosine, 111 bases upstream of the ATG translation start codon. The putative CAAT and TATA boxes were identified at -115 and -33 bp, respectively, with the mRNA cap site designated as +1. The barley nitrate reductase gene coding region strongly favors G or C in the third codon position.

Base Sequence

Optimization of the hygromycin B resistance-conferring gene as a dominant selectable marker in mammalian cells.

The HyR gene, conferring resistance to hygromycin B (Hy), has been modified for optimal expression in mammalian cells. Modifications to the HyR gene and its expression cassette include: (1) removal of all upstream start codons, (2) conversion of the region around the start codon to the consensus sequence associated with efficient translation initiation, and (3) removal of downstream splice donor and acceptor sequences. The resulting HyR gene is an efficient dominant selectable marker that is useful for studies requiring resistance from a low-copy-number gene driven by a promoter of moderate strength. The HyR gene was also tested for its compatibility with BPV vectors. Mouse C127 cells harboring pHyR-BPV plasmids exhibited properties of BPV-transformed cells and were resistant to toxic levels of Hy. The vectors were stable as episomes and present in high copy. The HyR gene thus joins the NmR (neo) gene as the only dominant selectable markers that are known to be compatible with BPV replication.

Animals

The reverse transcriptase gene of cauliflower mosaic virus is translated separately from the capsid gene.

Cauliflower mosaic virus (CaMV) possesses start codons at the beginning of its reverse transcriptase (RT) gene (ORF V) suggesting that, unlike in retroviruses and retrotransposons, it is translated independently from the capsid gene (ORF IV). To test this hypothesis a mutational analysis of the CaMV ORF IV/V overlapping region was performed. Mutants in which both ORFs are separated by stop codons in all three reading frames are viable and stable, while mutations affecting the first two AUG codons of ORF V are either lethal or unstable, giving rise to true and second site reversions. Mutants in which the AUG codons were replaced by ACG or AAG reverted only slowly and ACG could direct the synthesis of small amounts of reporter enzyme in transfected plant protoplasts, showing that this codon can act in plant cells as a weak start codon. CaMV has apparently developed a strategy for translation of the RT gene different from that in retroviruses and retrotransposons, but similar to that of hepadnaviruses, another group of pararetroviruses. The separate translation of the RT gene as a common feature of pararetroviruses might reflect the difference in their life cycle in comparison with retroviruses.

Base Sequence

Bacteriophage T4 gene 21 encodes two proteins essential for phage maturation.

The T4 prohead protease (T4 PPase) is the key enzyme in the morphopoietic pathway of the T4 phage head. It is responsible for the proteolytic processing of all head proteins allowing protein rearrangement and head expansion. To study its biochemistry and gene regulation, T4 gene 21 was cloned into an expression vector under the control of the inducible tac promoter. Two proteins of apparent molecular weights of 21.5 and 27.5 kDa were detected after induction. These proteins are synthesized using two different start codons in the same reading frame. Destruction of either start codon resulted in the loss of the respective protein. Complementation experiments with bacteriophage T4 21(-)-infected cells showed that both proteins are functional in vivo and essential for T4 phage assembly.

Base Sequence

Purification and characterization of an endoglucanase from Streptomyces lividans 66 and DNA sequence of the gene.

The endoglucanase isolated from culture filtrates of Streptomyces lividans IAF74 was shown to have an Mr of 46,000 and a pI of 3.3. The specific enzyme activity of 539 IU/mg, determined by the reducing assay method on carboxymethyl cellulose, is among the highest reported in the literature. The cellulase showed typical endo-type activity when reacting on oligocellodextrins. Optimal enzyme activity was obtained at 50 degrees C and pH 5.5. The kinetic constants for this endoglucanase, determined with carboxymethyl cellulose as the substrate, were a Vmax of 24.9 IU/mg of enzyme and a Km of 4.2 mg/ml. Activity was found against neither methylumbelliferyl- nor p-nitrophenyl-cellobiopyranoside nor with xylan. The DNA sequence contains one possible reading frame validated by the N terminus of the mature purified protein. However, neither ATG nor GTG starting codons were identified near the ribosome-binding site. A putative TTG codon was found as a good candidate for the start codon. Comparison of the primary amino acid sequence of the endoglucanase of S. lividans revealed that the N terminus contains a bacterial cellulose-binding domain. The catalytic domain at the C terminus showed similarity to endoglucanases from a Bacillus sp. Thus, the endoglucanase CelA belongs to family A of cellulases as described before (N. R. Gilkes, B. Henrissat, D. G. Kilburn, R. C. Miller, Jr., and R. A. J. Warren, Microbiol. Rev. 55:303-315, 1991.

Amino Acid Sequence

Development of a prokaryotic expression vector that exploits dicistronic gene organization.

For unknown reasons, levels of expression of foreign genes inserted into expression vectors in Escherichia coli have frequently been undetectable. The most critical step in the successful production of foreign proteins seems to be the initiation of translation. Since most prokaryotic genes are transcribed in a polycistronic form, we have devised a new prokaryotic expression system utilizing dicistronic gene organization. Downstream from a strong promoter and the gene encoding glutathione S-transferase from Schistosoma japonicum, various foreign genes were connected via a ribosome-binding site, a stop codon and a start codon. The VH domain of an immunoglobulin fused to the alpha subunit of tryptophan synthase, FK506-binding protein, cyclophilin, and a domain of a major histocompatibility complex antigen were successfully produced in E. coli as discrete polypeptides by this method.

Amino Acid Isomerases

Characterization of the human N-CAM promoter.

In contrast with the complex series of splicing choices that generate the various membrane-associated isoforms of the neural cell-adhesion molecule alternative splicing of 5' exons does not contribute to additional molecular diversity. A single regulatory unit in genomic DNA, mapping to a 5 kb restriction-endonuclease-HindIII fragment, controls the expression of all major RNA size classes. DNA sequence analysis of a 2 kb fragment spanning the two major identified transcriptional initiation sites (194 and 188 bp from the ATG codon) and translation start codon indicates that the regulatory unit does not possess classical TATA or CCAAT motifs. The region of the putative promoter exhibits a GC-rich content and a high frequency of the dinucleotide CpG, both characteristics of a HTF(HpaII tiny fragments)-island. Introduction of deletion-mutant chimaeric-gene constructs into human and rodent N-CAM-expressing cell lines defines an active promoter region of 467 bp (-144 to -611 bp from the ATG codon). This region of genomic DNA contains consensus sites for the interaction of known transcriptional factors.

Animals

Conservation in the 5' flanking sequences of transcribed members of the Caenorhabditis elegans major sperm protein gene family.

The major sperm proteins (MSPs) are encoded in the Caenorhabditis genome by a multigene family with more than 50 genes dispersed in small clusters at three chromosomal loci. In spite of their dispersed locations, all of the MSP genes appear to be expressed at the same time exclusively in the testis, indicating co-ordinate temporal and spatial regulation of these dispersed genes. Many of the MSP genes must be transcribed, because RNA hybridization with gene-specific probes showed that individual genes each contribute less than 3% to the total poly(A)+ RNA, and 13 out of 14 sequenced cDNAs came from different genes. Primer extension assays from MSP mRNA showed that most of the MSP mRNAs must be initiated at position -35 from the translation start codon. Extensive similarity was found in the first 100 nucleotides of genomic sequence flanking the start codons of ten MSP genes from different chromosomal locations. All MSP genes contained a consensus ribosome binding site, a consensus TATA homology 27 nucleotides distal to the site of mRNA initiation, and ten highly conserved nucleotides adjacent to the site of initiation. All the MSP genes contained the sequence AGATCT located approximately 65 nucleotides upstream from the transcriptional start, but little or no similarity was found more distal to this. Some of these conserved sequences may be cis-acting control elements that ensure the cell and temporal specificity of transcription of these co-ordinately regulated genes.

Animals