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PubMed2000

Influence of the Theiler's virus L* protein on macrophage infection, viral persistence, and neurovirulence.

The genome of picornaviruses contains a large open reading frame (ORF) translated as a precursor polypeptide that is processed to yield all the proteins necessary for the viral life cycle. In persistent but not in neurovirulent strains of Theiler's virus, an overlapping ORF encodes an additional 18-kDa protein called L*. We confirmed previous work showing that the L* ORF of persistent strains facilitates the infection of macrophage cell lines, and we present evidence that this effect is due to the L* protein itself rather than to competition for the translation of the two overlapping ORFs. The introduction of an AUG codon to restore the L* ORF of the neurovirulent GDVII strain also enhanced the infection of macrophages, in spite of the divergent evolution of this protein. The presence or the absence of the L* AUG initiation codon had only a weak influence on the neurovirulence of the GDVII strain and on the persistence of the DA1 strain. The results obtained with DA1 in vivo contrast with the results reported previously for DAFL3, another molecular clone of the same virus strain, where the AUG-to-ACG mutation of the L* initiation codon totally blocked viral persistence (G. D. Ghadge, L. Ma, S. Sato, J. Kim, and R. P. Roos, J. Virol. 72:8605-8612, 1998). Thus, a factor that is critical for the persistence of a given clone of Theiler's virus is dispensable for the persistence of a closely related clone, indicating that different adjustments in the expression of persistence determinants occur in related viral strains.

Animals↗
PubMed1999

Non-AUG initiation of AGAMOUS mRNA translation in Arabidopsis thaliana.

The MADS box organ identity gene AGAMOUS (AG) controls several steps during Arabidopsis thaliana flower development. AG cDNA contains an open reading frame that lacks an ATG triplet to function as the translation initiation codon, and the actual amino terminus of the AG protein remains uncharacterized. We have considered the possibility that AG translation can be initiated at a non-AUG codon. Two possible non-AUG initiation codons, CUG and ACG, are present in the 5' region of AG mRNA preceding the highly conserved MADS box sequence. We prepared a series of AG genomic constructs in which these codons are mutated and assayed their activity in phenotypic rescue experiments by introducing them as transgenes into ag mutant plants. Alteration of the CTG codon to render it unsuitable for acting as a translation initiation site does not affect complementation of the ag-3 mutation in transgenic plants. However, a similar mutation of the downstream ACG codon prevents the rescue of the ag-3 mutant phenotype. Conversely, if an ATG is introduced immediately 5' to the disrupted ACG codon, the resulting construct fully complements the ag-3 mutation. The AG protein synthesized in vitro by initiating translation at the ACG position is active in DNA binding and is of the same size as the AG protein detected from floral tissues, whereas AG polypeptides with additional amino-terminal residues do not appear to bind DNA. These results indicate that translation of AG is initiated exclusively at an ACG codon and prove that non-AUG triplets may be efficiently used as the sole translation initiation site in some plant cellular mRNAs.

AGAMOUS Protein, Arabidopsis↗
PubMed1992

Negative autoregulation of the neu gene is mediated by a novel enhancer.

In an attempt to study potential feedback regulation of the neu oncogene, we have found that the neu oncogene product specifically represses its own promoter activity. Deletion analysis indicated a 140-bp region (nucleotides -312 to -173 relative to the ATG initiation codon) in the rat neu promoter responsible for neu autorepression. Gel shift assays and methylation interference analysis further demonstrated that a GGTGGGGGGG sequence (nucleotides -243 to -234 relative to the ATG initiation codon) in this 140-bp region interacts with specific protein complexes. The GGTGGGGGGG sequence (GTG element), which functions as an enhancer, is sufficient to cause neu-mediated repression in a heterologous promoter. Furthermore, it produces different gel shift patterns with nuclear extracts from neu-transformed cell lines and their parental lines, suggesting that a transcriptional factor(s) interacting with this enhancer element has been perturbed by the introduction of neu. Taken together, the data presented in this report show that (i) the neu oncogene product autorepresses its own promoter, (ii) the neu promoter contains a novel enhancer, and (iii) neu autorepression is mediated through this enhancer, likely by inhibition of the enhancer activity.

Animals↗
PubMed1991

Nucleotide sequence of celC307 encoding endoglucanase C307 of Clostridium sp. strain F1.

The celC gene, encoding endoglucanase C, of Clostridium thermocellum was recently sequenced while a promoter region was not identified. In this study, the nucleotide sequence of celC307 of Clostridium sp. strain F1 was identified and compared with that of the C. thermocellum gene. The open reading frame was composed of 1029 nucleotides and the deduced amino acid sequence corresponded to a protein of a molecular weight of 40,905. We identified promoter sequences (TGGACA and TATAAT) at a position about 150 nucleotides upstream of the initiation codon. Six substitutions were found in the coding region, 3 leading to amino acid replacements. Five substitutions and 1 deletion of a nucleotide were found in the region upstream of the initiation codon, 1 present at the promoter sequence. Overproduction of endoglucanase C307 (EGC307) in Escherichia coli strongly inhibited the cell growth of the host strain. Around 50% of EGC307 produced in E. coli was detected in the periplasmic fraction. The N-terminal amino acid sequence suggested that this protein was exported into the periplasm without processing of a signal peptide.

Amino Acid Sequence↗
PubMed1988

Structure of the rabbit fast-twitch skeletal muscle Ca2+-ATPase gene.

We have isolated two genomic clones which together encode the Ca2+-ATPase of rabbit fast-twitch skeletal muscle sarcoplasmic reticulum. One of the two 16.5 kilobase (kb) genomic inserts in the lambda phage vector Charon 4A contains 23 exons extending from the polyadenylation site at the 3' end of the ATPase gene to within 38 nucleotides of the translation initiation codon in the 5' exon. An overlapping genomic insert of 16.5 kb contains the remainder of the 5' exon and a further 8 kb of upstream sequence. S1 nuclease mapping and primer extension analysis of the 5' end of the Ca2+-ATPase mRNA indicate that the transcription initiation site is located 185 base pairs (bp) upstream of the translation initiation codon. A "TATA" box (CA-TAAA) was found at position -30 and the sequence CCAAT was found at position -78 relative to the transcription initiation site. In a previous study (Brandl, C. J., de Leon, S., Martin, D. R., and MacLennan, D. H. (1987) J. Biol. Chem. 262, 3768-3774) cDNAs for neonatal and adult forms of the fast-twitch Ca2+-ATPase were shown to encode different carboxyl-terminal sequences, presumably as a result of alternative splicing. We have now found that these different DNA sequences encoding different carboxyl-terminal sequences are located in different exons. Exon boundaries of the Ca2+-ATPase gene did not correlate well with proposed domain boundaries for the Ca2+-ATPase protein. The locations of exon/intron boundaries were only partially conserved between the Ca2+-ATPase gene and a Na+/K+-ATPase gene (Ovchinnikov, Y. A., Monastyrskaya, G. S., Broude, N. E., Allikmets, R. L., Ushkaryov, Y. A., Melkov, A. M., Smirnov, Y. V., Malyshev, I. V., Dulubova, I. E., Petrukhin, K. E., Gryshin, A. V., Sverdlov, V. E., Kiyatkin, N. I., Kostina, M. B., Modyanov, N. N., and Sverdlov, E. D. (1987) FEBS Lett. 213, 73-80) and they did not follow closely the boundaries of amino acid sequences that are highly conserved among a group of ion transport ATPases.

Amino Acid Sequence↗
PubMed2000

A family of multifunctional thiamine-repressible expression vectors for fission yeast.

A series of thiamine-repressible shuttle vectors has been constructed to allow a more efficient DNA manipulation in Schizosaccharomyces pombe. These high-copy-number vectors with regulatable expression (pJR) are based on the backbone of the pREP-3X, pREP-41X and pREP-81X plasmids. The pJR vectors are all uniform in structure, containing: (a) sequences for replication (ori) and selection (AmpR) in Escherichia coli; (b) the f1 ori sequence of the phage f1 for packaging of ssDNA, making them suitable for site-directed mutagenesis; and (c) the ars1 sequence for replication in S. pombe. The pJR vectors differ among them in: (a) the selectable marker (Saccharomyces cerevisiae LEU 2 gene, which complements S. pombe leu1- gene and S. pombe ura4+ and his3+ genes); (b) the thiamine-repressible nmt1 promoter (3X, 41X and 81X with extremely high, moderate or low transcription efficiency, respectively); and (c) the multiple cloning site (two multiple cloning sites, with 12 restriction sites each). The expression level of the pJR vectors has been analysed using the beta-galactosidase gene as reporter. Three levels of expression for each nmt1 promoter version, with any selectable marker and for either repressed or induced conditions, have been found. The expression is dependent on the distance to the initiation codon, varying from 0.001 to 15 times the activity characterized for the pREP plasmids. Also, the gene expression has been found to be extremely sensitive to the nucleotide sequence prior to the initiation codon, being up to 50-fold higher with an A/T sequence than with a G/C sequence. Finally, the beta-galactosidase mRNA levels were found to be similar in each nmt1 series, suggesting a translational effect on gene expression. As a result, any of these 18 new vectors allow performing gene expression in fission yeast, as well as a more versatile cloning, sequencing and mutagenesis, directly in the plasmid without the need for subcloning into intermediary vectors.

Base Sequence↗
PubMed1997

Structure of catechol 2,3-dioxygenase gene encoded in TOM plasmid of Pseudomonas cepacia G4.

The catechol 2,3-dioxygenase is an extradiol-type dioxygenase which cleaves the C-C bond at the meta position of catechol to form 2-hydroxymuconic semialdehyde. A catechol 2,3-dioxygenase gene (tomB) in the TOM plasmid of P. cepacia G4 has been cloned and its nucleotide sequence was analyzed. The enzyme gene consisted of 945 base pairs with an ATG initiation codon and a TGA termination codon which can encode a polypeptide of molecular weight 35 kDa containing 314 amino acid residues, and a putative ribosome-binding sequence was identified at approximately 10 nucleotides upstream of the initiation codon. The deduced amino acid sequence of catechol 2,3-dioxygenase from P. cepacia G4 exhibited 79-82% homologies with those of 3-methylcatechol 2,3-dioxygenase of P. putida UCC2 and catechol 2,3-dioxygenase of P. pickettii PKO1.

Amino Acid Sequence↗
PubMed1989

Transcriptional analysis of the CDC7 protein kinase gene of Saccharomyces cerevisiae.

The 5' flanking region of the CDC7 gene of Saccharomyces cerevisiae has been sequenced to a point 797 nucleotides upstream of the putative translational initiation codon (designated +1). The sequence reveals a number of symmetry elements between -100 to -380 and two blocks of high local AT content between -29 to -75 and -112 to -144. Transcription initiates heterogeneously at about 10 discrete sites up to 110 nucleotides upstream of the putative translational initiation codon. Some minor transcriptional start sites were also observed between the ATG at +1 and a second in-frame ATG at +55, suggesting that CDC7 may also be translationally heterogeneous. Deletion analysis of the CDC7 upstream region has shown that the gene lacks a functional TATA box, and has identified a 30bp element that is necessary for normal CDC7 promoter function during mitosis. This motif has significant homology with a component of the c-fos promoter which acts to regulate c-fos expression by binding a transcription activating factor. The results suggest that the 30bp motif may play a similar role in regulating CDC7 expression and that there may be similarities between factors that regulate CDC7 expression in yeast and c-fos expression in vertebrate cells.

Amino Acid Sequence↗
PubMedDate not supplied

Molecular cloning and developmental expression of the major fibrous sheath protein (FS 75) of rat sperm.

The fibrous sheath (FS) is a cytoskeletal structure that encases the axoneme in the principal piece of the spermatozoon tail. In the rat, it is composed of several proteins, of which a 75-kDa polypeptide (FS 75), as estimated by PAGE, is the most prominent. The objectives of this study were to clone and sequence this protein and to characterize its transcriptional and translational origins during spermatogenesis. Initially, we isolated two overlapping cDNA segments that encoded a large part of the FS 75 protein but lacked the initiation codon for translation. Both clones were obtained by screening a rat testicular phagemid cDNA library with an anti-FS 75 polyclonal antibody. An upstream portion of the FS 75 mRNA containing the initiation codon was obtained by polymerase chain reaction with a pair of specific primers. Accounting for the overlap in all segments, 2786 nt of an approximately 3-kb FS 75 mRNA was obtained. The amino acid sequence of the longest possible open reading frame of the rat FS 75 was found to be similar to two previously cloned variants of the major FS polypeptide of mouse spermatozoa. Sequence analysis of the rat FS cDNA revealed anchoring kinase A protein domains and several kinase phosphorylation sites, supporting the idea that this protein plays a crucial role in the motility of spermatozoa. The presence of a potential N-myristoylation site suggests that this protein may covalently bind to the inner leaflet of the plasma membrane (PM), which in turn may explain the close association of the FS and PM from early development. Developmental northern blot analysis and in situ hybridization revealed that the FS 75 mRNA is haploid expressed, with an abundant level of mRNA in late round spermatids. Maximum levels of the FS 75 polypeptide, as determined by immunocytochemistry, correlated with a rapid decline in corresponding mRNA levels in step 14-16 spermatids. Since transcription termination occurs several steps earlier, the bulk of FS 75 mRNA appears to be translationally regulated.

Amino Acid Sequence↗
PubMed2005

Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems.

A widely distributed family of small regulators, called C proteins, controls a subset of restriction-modification systems. The C proteins studied to date activate transcription of their own genes and that of downstream endonuclease genes; this arrangement appears to delay endonuclease expression relative to that of the protective methyltransferase when the genes enter a new cell. C proteins bind to conserved sequences called C boxes. In the PvuII system, the C boxes have been reported to extend from -23 to +3 relative to the transcription start for the gene for the C protein, an unexpected starting position relative to a bound activator. This study suggests that transcript initiation within the C boxes represents initial, C-independent transcription of pvuIICR. The major C protein-dependent transcript appears to be a leaderless mRNA starting farther downstream, at the initiation codon for the pvuIIC gene. This conclusion is based on nuclease S1 transcript mapping and the effects of a series of nested deletions in the promoter region. Furthermore, replacing the region upstream of the pvuIIC initiation codon with a library of random oligonucleotides, followed by selection for C-dependent transcription, yielded clones having sequences that resemble -10 promoter hexamers. The -35 hexamer of this promoter would lie within the C boxes. However, the spacing between C boxes/-35 and the apparent -10 hexamer can be varied by +/-4 bp with little effect. This suggests that, like some other activator-dependent promoters, PpvuIICR may not require a -35 hexamer. Features of this transcription activation system suggest explanations for its broad host range.

DNA Restriction-Modification Enzymes↗
PubMed1988

Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA.

We have identified the binding site on the bacteriophage T4 gene 32 mRNA responsible for autogenous translational regulation. We demonstrate that this site is largely unstructured and overlaps the initiation codon of gene 32 as previously predicted. Co-operative binding of gene 32 protein to this site specifically blocks the formation of 30 S-tRNA(fMet)-gene 32 mRNA ternary complexes and initiation of translation. The translational operator is bound co-operatively by gene 32 protein and this binding is facilitated by a nucleation site far upstream from the initiation codon. A similar unstructured mRNA lacking this nucleation site is also bound co-operatively, but only at concentrations of gene 32 protein higher than those needed to repress binding of ribosomes to the gene 32 mRNA. Some sequence-specific interactions may also influence this binding. Comparison of the bacteriophage T2, T4 and T6 gene 32 operator sequences leads us to propose that the nucleation site is a pseudoknot.

Base Sequence↗
PubMed2006

Association between functional FABP2 promoter haplotype and type 2 diabetes.

Fatty acid-binding protein 2 (FABP2) is a cytosolic protein expressed exclusively in epithelial cells of the small intestine. Some, albeit not conclusive, evidence indicates that the Thr-allele of FABP2 Ala54Thr polymorphism is associated with type 2 diabetes. More recently, common FABP2 promoter polymorphisms have shown association with postprandial increase of triglycerides, body composition and plasma lipid levels. Therefore, we reasoned that variants in the FABP2 promoter may also predispose to type 2 diabetes mellitus. In our Caucasian study population, we found three SNPs and three insertion-deletion polymorphisms that are in complete linkage disequilibrium defining promoter haplotype A and B within 1kb 5' of the FABP2 initiation codon. Haplotype calculations indicated that the FABP2 promoter and Ala54Thr variants were strongly linked. Functional analysis of promoter fragments demonstrated that haplotype difference is caused by polymorphisms within 260 bp downstream of the FABP2 initiation codon. Using a prospective case-control study nested within the EPIC-Potsdam cohort of 192 incident type 2 diabetes cases and 384 sex-/age-matched controls, male subjects carrying the FABP2 haplotype B allele showed significantly decreased risk of type 2 diabetes when adjusted for BMI (OR = 0.50, 95 % CI = 0.28 - 0.87, p < 0.05) and additional covariates (OR = 0.42, 95 % CI 0.22 - 0.81, p < 0.01). Further adjustment for the Ala54Thr polymorphism revealed an OR of 0.18 (95 % CI 0.06 - 0.49, p < 0.001). Similarly, Ala/Ala homozygote males carrying the promoter haplotype B had decreased risk (0.33, 0.11 - 0.94, p < 0.05) of type 2 diabetes after stratification for the Ala54Thr polymorphism. FABP2 promoter haplotypes or genotype combinations defined by the promoter and Ala54Thr polymorphism were not associated with BMI, body fat, leptin, HbA (1c), total cholesterol or HDL. In conclusion, our findings suggest that the functional FABP2 promoter haplotype may contribute to type 2 diabetes in a sex-specific manner.

Adult↗
PubMed1983

Translation of insulin-related polypeptides from messenger RNAs with tandemly reiterated copies of the ribosome binding site.

Plasmids have been constructed containing reiterated copies of a 66 bp fragment, loosely referred to as the ribosome binding site, that includes the AUG initiator codon of preproinsulin. The extreme test involved plasmid 255/17, which carried four tandem copies of the ribosome binding site, with all four AUG triplets in the same reading frame as the preproinsulin coding sequence downstream. Initiation at any potential start site would generate a polypeptide precipitable with anti-insulin antiserum, and its size would reveal the AUG(s) active in initiation. One insulin-related polypeptide was synthesized in cells transfected by p255/17; its size corresponded to the product initiated at the first ribosome binding site in the tandem array. Inasmuch as the three downstream AUG triplets, which are not used, occur in a sequence context identical with that around the 5'-proximal AUG triplet, which is used, the position of an AUG triplet relative to the 5' end of the mRNA appears to be important in identifying it as a functional initiator codon.

Base Sequence↗
PubMed1998

Sequence analysis of the 5'-flanking region of the gene encoding human HOXA-7.

We have isolated and characterized the immediate 5'-flanking region (886 bp) of the gene encoding human HOXA-7. When the total sequence was compared with those of mice, 93% of the 3' 518 bp (nt 370-886) sequences were identical, in which the 245 bases just preceding the AUG initiator codon (nt 614) was as highly conserved as in the coding region (nt 614-886). Sequences further upstream (nt 1-370) by comparison were highly diverged. In the 245 bp region, 8 stop and 3 initiation (including the initiator) codons were located, and a 50-aa long presumptive polypeptide was encoded. Nucleotide sequence analysis revealed three Sp1 and one AP2 binding sites, as well as one CAAT box. However, there was no consensus sequence for a TATA box in the 5' flanking region. One RARE repeat, one krox20 and three Hox-PBC binding sites were detected. Since many of the factor recognition sites were located in the immediate 5' flanking sequences of a highly-conserved region, it might be speculated that a regulatory mechanism for Hox gene expression is conserved throughout the evolution and one possible mechanism could be at the post-translational level.

5' Untranslated Regions↗
PubMed1996

The trpF nucleotide sequence and its promoter analysis in Pseudomonas aeruginosa.

The nucleotide sequence of the gene for the phosphoribosyl anthranilate isomerase (PRAI) (trpF) in Pseudomonas aeruginosa was determined. The gene encoded a polypeptide of 211 amino acid residues and its initiation codon was UUG. Northern hybridization analysis showed only one transcript for trpF (about 700 nucleotides). Primer extension analysis revealed three transcription start sites which were at positions 52, 55 and 57 bases upstream of the initiation codon. A highly GC-rich 9-base-pair inverted repeat with 5-base-pair spacing was found upstream of a putative Shine-Dalgarno sequence. This inverted repeat could form a 23-nucleotide stem-loop structure in the transcript. Deletion of the inverted repeat slightly decreased the promoter activity of trpF. The presence of tryptophan had no effect on transcription of trpF.

Aldose-Ketose Isomerases↗
PubMed1998

Human sex hormone-binding globulin gene expression in transgenic mice.

The sex hormone-binding globulin gene (shbg) is expressed in the liver and testis as well as in several other tissues that play important roles in reproduction. Expression of shbg in the human liver results in the production of plasma sex hormone-binding globulin (SHBG), which regulates the bioavailability of sex steroids in the blood. Although shbg is not expressed in rodent livers postnatally, it gives rise to the androgen-binding protein in their testes upon sexual maturation. Human shbg is also expressed in the testis, but its products and their function are less well characterized. To study the expression of human shbg in different tissues and the consequences of overexpressing this gene in vivo, we have produced several lines of mice containing approximately 11-kilobase (kb; shbg11) or 4.3-kb (shbg4) human shbg genomic fragments that comprise all eight exons encoding SHBG as well as approximately 6 kb or approximately 0.9 kb of 5'-flanking DNA, respectively. Northern blots indicated that human shbg transcripts were most abundant in liver, kidney, and testis of the shbg11 mice. The 4.3-kb shbg transgenes were expressed at similar levels in liver and kidney, but the abundance of human shbg transcripts in their testes was much lower than that in shbg11 mice. Primer extension analysis indicated that transcription starts 60 bp from the translation initiation codon for SHBG in liver and kidney of shbg11 mice, and that the shbg transcripts in their testis are derived from a separate promoter flanking an alternative exon that replaces the exon containing the translation initiation codon for SHBG or androgen-binding protein. At the cellular level, the human shbg transgenes are expressed in clusters of hepatocytes located mainly within the periportal region of hepatic lobules and in the epithelial cells lining the proximal convoluted tubules of the kidney. This results in high levels of human SHBG in serum (1.45-1.72 nmol/ml) and urine (6-16 pmol/ml) of mature male shbg mice. The abundance and distribution of human shbg transcripts in the Sertoli cells of shbg11 mice vary throughout the spermatogenic cycle, with levels increasing in the Sertoli cell cytoplasm until stage VII of spermatogenesis and declining after stage IX. At stages X-XII of spermatogenesis, these transcripts concentrate at the adluminal compartment of the Sertoli cells, and this suggests that they have a role in the elongation phase of spermiogenesis. The presence of human SHBG in the blood of shbg transgenic mice may result in serum levels of testosterone that are 10-100 times higher than those in wild-type littermates. Despite this, their reproductive performance is normal, and there is no obvious phenotypic abnormalities even in animals homozygous for the transgenes.

Animals↗
PubMed1990

Isolation and characterization of non-muscle tropomyosin cDNAs of human and mouse origin.

Several cDNA clones of human and mouse non-muscle tropomyosin have been isolated. All the human clones possess a common 23 bp sequence immediate 5' of the initiation codon. However, in the further upstream regions, the nucleotide sequences diverge. Two of the mouse cDNA clones pPSI-8 and pPSI-14 have identical nucleotide sequence in the coding region sequenced. However, 5' of the initiation codon these clones have only 40 identical nucleotides and further upstream the nucleotide sequences diverge. Analysis of the genomic DNAs of mouse cells indicated the possibility of a common gene giving rise to both the tropomyosin cDNAs differing in their 5' ends.

Amino Acid Sequence↗
PubMed1995

A single base-pair change (ATG-->ATC) nullifies the activity of cytosolic fumarase in Saccharomyces cerevisiae.

A respiratory defective pet mutant (W303 delta FUM1) of Saccharomyces cerevisiae deficient in fumarase was transformed with the plasmid construct pG5/ST7. This plasmid contains the entire FUM1 gene with only a single base pair change (ATG-->ATC) confined to the putative second inframe translation initiation codon. While transformation of the fumarase deficient mutant with pG5/ST7 resulted in an elevation of fumarase activity in the mitochondria of the transformed strain, fumarase activity in the cytosol remained negligible his result indicated that the cytosolic fumarase isoenzyme is synthesized exclusively from the second translation initiation codon of FUM1. Results of RACE-PCR of the 5' ends of FUM1 transcripts confirmed that the FUM1 gene synthesizes two distinct species of transcripts. These data provide strong evidence for the synthesis and targeting of two fumarase isomers.

Base Composition↗