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At least 1,189 records · Page 66Linked to original sources
PubMed1989

Substitution of asparagine324 with aspartic acid in the Fc portion of mouse antibodies reduces their capacity for C1q binding.

The sequence of the heavy chain C region of mouse mutant IgG2a antibodies with reduced capacity for C1q binding but with retained ability for Fc receptor-mediated functions was determined by cDNA cloning and by mRNA sequencing. The specific mutation was found to be the substitution of asparagine324 with aspartic acid. Asparagine324 represents a new residue relating to the C1q-binding sites previously described.

Amino Acid Sequence↗
PubMed1995

1,25(OH)2D3-dependent regulation of calbindin-D28k mRNA requires ongoing protein synthesis in chick duodenal organ culture.

Organ culture of 19-day-old chick embryo duodena was utilized to evaluate the mechanism of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)-dependent calbindin-D28k (CaBP) expression. Duodenal CaBP and 1,25(OH)2D3 receptor (VDR) expression were assessed by Western blot analysis, while CaBP and VDR mRNA levels were determined by Northern blot analysis. In untreated duodena, both VDR protein and mRNA were present, while CaBP protein and mRNA were undetectable. Treatment of cultured duodena with 25 nM 1,25(OH)2D3 resulted in detectable CaBP mRNA after 4 h which continued to increase during a 24 h time period. Under these conditions, localization of [3H-1 beta]1 alpha,25(OH)2D3 in duodenal chromatin is rapid (< or = 30 min). Thus, the delayed accumulation of detectable CaBP mRNA cannot be explained by slow nuclear binding of 1,25(OH)2D3. The inclusion of 1.6 microM actinomycin D in the organ culture partially inhibited the 1,25(OH)2D3-regulated increase in CaBP mRNA, which implies that there is a transcriptional component involved in the increased CaBP mRNA levels. Similarly, quantitative polymerase chain reaction studies allowed the detection of CaBP pre-mRNA and mRNA sequences 1 h after hormone treatment, suggesting that CaBP gene transcription is initiated rapidly. Treatment of cultures with 36 microM cycloheximide 1 h prior to 1,25(OH)2D3 addition resulted in superinduction of VDR mRNA levels but sharply reduced CaBP steady-state mRNA levels. This dramatic reduction in CaBP mRNA reveals that 1,25(OH)2D3-mediated CaBP expression is dependent on ongoing protein synthesis. Thus, we propose that a labile auxiliary protein or other cofactor, which may or may not be 1,25(OH)2D3-dependent, is necessary for 1,25(OH)2D3-mediated CaBP gene transcription in chick duodena.

Animals↗
PubMed1995

The genes encoding subunit 3 of NADH dehydrogenase and ribosomal protein S12 are co-transcribed and edited in Pinus sylvestris (L.) mitochondria.

The nucleotide sequence of the region encoding NADH dehydrogenase subunit 3 and ribosomal protein S12 from Pinus sylvestris (L.) mitochondrial DNA (mtDNA) has been determined. A sequence comparison of this region with six individual cDNA clones prepared by RT-PCR revealed 35 C-to-T differences, showing the occurrence of RNA editing. All but one of these alterations in mRNA sequence change codon identities to specify amino acid better conserved in evolution. Most of these modifications take place within the nad3 gene changing 20% of the amino-acid sequence, which is much more than in angiosperms. Of six cDNA clones investigated, four clones of nad3 were differentially edited, but the editing of the rps12 sequences was identical. As in angiosperms, the two genes are separated by a short sequence of 52 bp, which is not edited. Two transcripts of about 0.9 kb and 1.2 kb, each encoding both proteins, have been detected by Northern hybridisation. The hybridisation of nad3 and rps12 probes with pine mtDNA digested with different restriction enzymes indicates that both genes are present in a single copy in pine mtDNA. The analysis of PCR amplification products with gene-specific primers shows a conserved order of these genes in a wide range of gymnosperms.

Amino Acid Sequence↗
PubMed1984

Superinduction of human interleukin-2 messenger RNA by inhibitors of translation.

Stimulation of human lymphocytes with phytohemagglutinin results in the induction of messenger RNA encoding interleukin-2 (IL-2), a lymphokine possessing immuno-regulatory properties. We have previously demonstrated a dramatic superinduction of the formation of IL-2 and of biologically active IL-2 mRNA in the presence of cycloheximide, an inhibitor of translation. These findings suggested the involvement of a labile protein repressor in the regulation of human IL-2 gene expression. Here, we show a commensurate superinduction of IL-2 mRNA sequences by three additional inhibitors of protein synthesis with distinct modes of action: T-2 toxin, pactamycin, and sparsomycin. These results strengthen the concept that a labile protein controls the formation of mature IL-2 mRNA. They tend to eliminate the possibility that the superinduction phenomenon observed in the presence of cycloheximide is due to its action on a process other than translation.

Cells, Cultured↗
PubMed1995

Cloning and structure of the gene encoding the human N-methyl-D-aspartate receptor (NMDAR1).

The complete gene encoding the human N-methyl-D-aspartate receptor subunit NR1 (NMDAR1) has been isolated on a single cosmid clone. The gene is composed of 21 exons distributed over a total length of about 31 kb. More than 24 kb were sequenced. Exons 4, 20 and 21 are identical in their amino-acid sequence to those exons that are subject to alternative splicing in rat, indicating that all eight NMDAR1 isoforms found in rat will also be expressed in the human brain. Computer analysis of the pre-mRNA sequence revealed no secondary structures stable enough to explain alternative splicing. We suggest that cell-specific factors control expression of different isoforms. The promoter region contains two perfect copies of the recognition sequence for the Drosophila even-skipped protein, indicating that the developmentally regulated expression of NMDAR1 is controlled by a homeobox protein. The complete cosmid clone covering NMDAR1 was mapped to chromosome 9q34.3-qter by fluorescent in situ hybridization (FISH). The telomeric location is supported by an imperfect (CA)n repeat homologous to a subtelomeric repeat on chromosome 16p.

Alternative Splicing↗
PubMed1996

Identification and characterization of an RNA specific primer for human tumor necrosis factor receptor I (TNFR-I).

An RNA specific primer amplified TNFR-I cDNA from cellular RNA by single-tube (ST) RT-PCR without interfering with the presence of genomic DNA of cell was identified. The primer detected TNFR-I from 1 ng of cellular RNA by ST RT-PCR, and was not cross-reacted with TNFR-II despite of the homologous sequence between TNFR-I and -II. In addition, the mechanism of the RNA specificity of the primer was investigated. An intron of 0.43 kb was inserted in the 5'-925 of TNFR-I mRNA sequence. The result corresponded with the previous determination of TNFR-I gene structure. Thus, it appears that the RNA specificity of the primer might be resulted from the antisense primer hybridizing to exon-intron junction. Owing to its high sensitivity and specificity to TNFR-I RNA, the RNA specific primer may be potentially utilized for the determination of human TNFR-I gene expression by in situ RT-PCR.

Antigens, CD↗
PubMed1983

Structural proteins of adenovirus-associated virus: subspecies and their relatedness.

Capsids of adenovirus-associated virus (AAV) are known to contain three major structural proteins (A, B, and C). We have further resolved distinct subspecies of two of the major AAV proteins (two forms of protein A and four forms of protein C) which were found in both AAV1 and AAV2 serotypes. All subspecies were accurately synthesized in a cell-free translation system programmed with RNA isolated from infected cells. Analysis of virion proteins from the autonomous parvovirus H1 did not reveal a comparable array of subspecies of its major components. Staphylococcal V8 protease digestion of C proteins from AAV1 and AAV2 yielded very different electrophoretic patterns, indicating a considerable difference between the C proteins of these two serotypes, despite a high degree of genomic homology and an overall similarity in the number and relative proportions of analogous capsid proteins. On the other hand, staphylococcal V8 protease digestion of isolated proteins A, B, and C of AAV2 showed an extensive overlap among these proteins, possibly equivalent to all of protein C. In conjunction with other data, these findings suggest that proteins A, B, and C arise from different in-frame initiation sites contained in mRNA sequences that are transcribed from the right half of the AAV genome. The heterogeneity of subspecies may be explained by a partial read through of several tandem termination codons near the 3' end of AAV mRNA.

Dependovirus↗
PubMed2000

Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways.

Several studies of the yeast Saccharomyces cerevisiae support differential regulation of heat shock mRNA (hs mRNA) and non-hs mRNA nuclear export during stress. These include the finding that hs mRNA export at 42 degrees C is inhibited in the absence of the nucleoporinlike protein Rip1p (also called Nup42p) (C. A. Saavedra, C. M. Hammell, C. V. Heath, and C. N. Cole, Genes Dev. 11:2845-2856, 1997; F. Stutz, J. Kantor, D. Zhang, T. McCarthy, M. Neville, and M. Rosbash, Genes Dev. 11:2857-2868, 1997). However, the results reported in this paper provide little evidence for selective non-hs mRNA retention or selective hs mRNA export under heat shock conditions. First, we do not detect a block to non-hs mRNA export at 42 degrees C in a wild-type strain. Second, hs mRNA export appears to be mediated by the Ran system and several other factors previously reported to be important for general mRNA export. Third, the export of non-hs mRNA as well as hs mRNA is inhibited in the absence of Rip1p at 42 degrees C. As a corollary, we find no evidence for cis-acting hs mRNA sequences that promote transport during heat shock. Taken together, our data suggest that a shift to 42 degrees C in the absence of Rip1p impacts a late stage of transport affecting most if not all mRNA.

Biological Transport↗
PubMedDate not supplied

The sugar beet mitochondrial gene for the ATPase alpha-subunit: sequence, transcription and rearrangements in cytoplasmic male-sterile plants.

We have characterized the mitochondrial atpA (the alpha subunit of F1-ATPase) gene from male-fertile cytoplasm (cv TK81-0) of sugar beet. The gene is 1518-bp long and encodes a polypeptide of 506 amino acids. The atpA mRNA sequence is modified by three C-to-U RNA editing events, all of which alter the encoded protein sequences. In order to examine the genome organization of the atpA locus in cytoplasmic male-sterile (CMS) sugar beet, atpA-containing clones were isolated from Owen CMS (TK81-MS) and a different source of CMS [I-12CMS(2)] cytoplasm respectively. The sequences of the atpA coding region from TK81-MS and I-12CMS(2) are identical to each other and to the corresponding TK81-0 sequence. However, the TK81-0 and TK81-MS loci diverge completely 47 bp upstream of the initiation codon, resulting in different 5' transcript termini for the two genes. On the other hand, the point of divergence between the TK81-0 and I-12CMS(2) atpA genes was found to occur after 393 bp 3' to the TAA stop codon. Our results also show the 3'-flanking sequences of I-12CMS(2) atpA to be present elsewhere in the mitochondrial genomes of TK81-0, TK81-MS and I-12CMS(2), suggesting the possible involvement of these repeated DNA elements in the sequence rearrangements.

Adenosine Triphosphatases↗
PubMed1998

Restricted tissue expression pattern of a novel human rasGAP-related gene and its murine ortholog.

The mammalian rasGAPs constitute a group of widely expressed proteins involved in the negative regulation of ras-mediated signaling. In this study we have isolated a novel human gene, RASAL (Ras GTPase-activating-like) and its murine ortholog, MRASAL which are most similar to the GAP1 family of rasGAP proteins, based upon the presence and organization of specific conserved domains. Full-length human and murine mRNA sequences are predicted to encode 804 and 799 amino acid polypeptides, respectively. Sequence analysis of these two proteins revealed the presence of two N-terminal calcium-dependent phospholipid binding C2 domains, a conserved GAP related domain (GRD) and a C-terminal pleckstrin homology (PH) domain. Northern blot and mRNA in situ hybridization analyses indicate that RASAL, in contrast to other mammalian rasGAP proteins, has a limited expression pattern; RASAL is highly expressed in the follicular cells of the thyroid and the adrenal medulla and expressed at lower levels in brain, spinal cord and trachea. Human RASAL has been localized by radiation hybrid mapping to chromosome 12q23-24.

Amino Acid Sequence↗
PubMed1990

Endonucleolytic cleavage of a maternal homeo box mRNA in Xenopus oocytes.

We have identified a messenger RNA (mRNA) sequence from a Xenopus homeo box-containing gene that is the target for a sequence-specific endoribonuclease in vivo. Synthetic RNA transcribed from an allele of the maternal gene Xlhbox2B is efficiently cleaved when injected into Xenopus oocytes. The cleavage sequence lies between the protein-coding region and a 600-base 3'-untranslated region. Intermediates in degradation are readily observed: Both the 5' and 3' products of cleavage are recovered, thus showing that the cleavage activity is an endonuclease. When a 90-base region of the Xlhbox2B sequence is inserted into a second homeo box RNA that is normally stable, it is sufficient to confer an identical cleavage reaction on the hybrid RNA. The cleaved region contains a repeated sequence motif and is cut at multiple sites. Inhibition of translation does not affect the rate or extent of cleavage, while the coinjection of antisense RNA complementary to the 90-base region completely blocks the reaction. Because most mRNAs are not found on polysomes during oogenesis, translation-independent cleavage at such sites may provide a novel post-transcriptional mechanism to regulate the amount of mRNA available for embryogenesis.

Alleles↗
PubMed1997

Improving the efficiency of the genetic code by varying the codon length--the perfect genetic code.

The function of DNA is to specify protein sequences. The four-base "alphabet" used in nucleic acids is translated to the 20 base alphabet of proteins (plus a stop signal) via the genetic code. The code is neither overlapping nor punctuated, but has mRNA sequences read in successive triplet codons until reaching a stop codon. The true genetic code uses three bases for every amino acid. The efficiency of the genetic code can be significantly increased if the requirement for a fixed codon length is dropped so that the more common amino acids have shorter codon lengths and rare amino acids have longer codon lengths. More efficient codes can be derived using the Shannon-Fano and Huffman coding algorithms. The compression achieved using a Huffman code cannot be improved upon. I have used these algorithms to derive efficient codes for representing protein sequences using both two and four bases. The length of DNA required to specify the complete set of protein sequences could be significantly shorter if transcription used a variable codon length. The restriction to a fixed codon length of three bases means that it takes 42% more DNA than the minimum necessary, and the genetic code is 70% efficient. One can think of many reasons why this maximally efficient code has not evolved: there is very little redundancy so almost any mutation causes an amino acid change. Many mutations will be potentially lethal frame-shift mutations, if the mutation leads to a change in codon length. It would be more difficult for the machinery of transcription to cope with a variable codon length. Nevertheless, in the strict and narrow sense of coding for protein sequences using the minimum length of DNA possible, the Huffman code derived here is perfect.

Algorithms↗
PubMed1982

Analysis of histone gene expression during the cell cycle in HeLa cells by using cloned human histone genes.

Although it is generally agreed that histone protein synthesis is restricted to the S phase of the cell cycle--and therefore parallels DNA replication--both transcriptional and posttranscriptional levels of control have been invoked. Using blot hybridization with several cloned genomic human histone sequences representing different histone gene clusters as probes, we have assessed the steady-state level of histone RNAs in the nucleus and cytoplasm of G1 and S phase HeLa S3 cells. The representation of histone mRNA sequences of G1 compared with S phase cells was less than 1% in the cytoplasm and approximately 1% in the nucleus. These data are consistent with transcriptional control, but we cannot completely dismiss the possibility that regulation of histone gene expression is, to some extent, mediated posttranscriptionally. If histone gene transcription does occur in G1, the RNAs must either be rapidly degraded or be transcribed to a limited extent compared with S phase. An unexpected result was obtained when a blot of cytoplasmic RNA from G1 and S phase cells was hybridized with lambda HHG 41 DNA (containing H3 and H4 human genomic histone sequences). Although hybridization with histone mRNAs was observed for RNAs from S phase but not from G1 cells, hybridization with a nonhistone RNA of approximately 330 nucleotides present predominantly in G1 was also observed.

Bacteriophage lambda↗
PubMed1993

Analysis of respiratory syncytial virus genetic variability with amplified cDNAs.

Antigenic and genetic heterogeneities exist within the two major antigenic groups of respiratory syncytial (RS) virus. We developed a polymerase chain reaction (PCR)-based assay that not only differentiates the two RS virus groups but allows distinctions within groups on the basis of changes in the nucleotide sequences, as revealed by restriction fragment analysis. In this assay, viral RNA served as a template for cDNA synthesis with extension from a synthetic oligonucleotide primer complementary to bases 164 to 186 in the F protein mRNA. For PCR amplification, two group-specific 5' primers were added. The two primers corresponded to the G protein mRNA sequence of group B (bases 10 to 30) or group A (bases 247 to 267) RS virus. Agarose gel electrophoresis readily discriminated the 1.1-kb group B and the 0.9-kb group A virus amplification products. All 47 viruses tested were assigned to the same group by both PCR and monoclonal antibody reaction pattern analysis. Restriction fragment analysis of the amplified DNAs revealed 12 restriction patterns for group A viruses and 7 restriction patterns for group B viruses, while the monoclonal antibody reaction patterns revealed seven patterns for group A viruses and 3 patterns for group B viruses. Most viruses with the same monoclonal antibody reaction patterns had different restriction patterns, and some viruses with the same restriction patterns had different monoclonal antibody reaction patterns. Thus, the results of the PCR assay concurred with the monoclonal antibody reaction pattern analysis for group classification of RS viruses, while the restriction fragment analysis identified greater diversity within groups than was seen with the monoclonal antibody analysis.

Antigens, Viral↗
PubMed1987

Novel V genes encode virtually identical variable regions of six murine monoclonal anti-bromelain-treated red blood cell autoantibodies.

The variable (V) region sequences of six immunoglobulin M (IgM, kappa) monoclonal autoantibodies that recognize bromelinized isologous red blood cells, obtained by fusions of peritoneal cells from NZB or CBA/J nonimmunized mice with BALB/c myeloma cells, were determined by direct mRNA sequencing. The V regions of the light chains (VL) are almost identical with one another, as are the V regions of the heavy chains (VH), which, however, differ by six linked-base substitutions, depending on the strain of mice producing the autoantibodies. Such variations may reflect allelic differences. The VH segments determined have no obvious correspondence to any VH genes identified so far. They may belong to the small VH group 4, where 73% homology, at the most, can be calculated at the protein level for codons 1 to 94. Alternatively, the VH regions may be members of a new group of VH sequences not previously found. The V kappa regions appear closely homologous to members of the V kappa-9 subgroup of myeloma proteins of unknown antigen-binding specificity. The joining segments, J kappa and JH, used by the autoantibodies investigated, originate from the J kappa 2 and JH1 germ-line gene segments, respectively. The nine base-long diversity segments, D, derive from one member of the germ-line D gene SP2 family.

Animals↗
PubMed1985

Coordinate regulation of mouse metallothionein I and II genes by heavy metals and glucocorticoids.

Regulation of the endogenous mouse metallothionein I and II (MT-I and MT-II) genes by heavy metals and glucocorticoids was studied in cultured mouse cells. Both mRNAs were measured simultaneously by solution hybridization with [3H]MT-I cDNA and [32P]MT-II cDNA, and the absolute amount of each mRNA was calculated by using a single-stranded M13 standard that contained both mRNA sequences. Both genes responded identically to different concentrations of metals (zinc, cadmium, and copper) and dexamethasone. Furthermore, the time courses of induction of both mRNAs were the same. However, under all conditions there was 1.2- to 1.9-fold more MT-I mRNA than MT-II mRNA. We conclude that both genes are regulated identically by receptors for glucocorticoids and metals but that the rate of transcription from the MT-I gene is slightly higher than from the MT-II gene.

Animals↗
PubMed1987

A mouse homeobox containing gene on chromosome 11: sequence and tissue-specific expression.

We have molecularly cloned a mouse homeobox containing gene by isolating cDNA and genomic clones. The gene is located in a previously described cluster on chromosome 11 (Hart et al. (1985) Cell 43, 9-18) and was identified as the Hox2.3 gene. We present the complete mRNA sequence of this gene and describe similarities to other homeobox containing genes, among which its human homologue, the cl gene. High expression of the Hox2.3 gene was found in kidney, testis, and spinal cord of adult mice, in the spinal cord of 12.5-17.5 day embryos and in differentiating EC cells depending on their treatment. Three different treatments of the pluripotent EC cell line P19, each leading to the induction of a specific differentiation pathway, resulted in all cases in induction of Hox2.3; however, major quantitative differences in this response were observed.

Amino Acid Sequence↗
PubMed1989

The Drosophila E74 promoter contains essential sequences downstream from the start site of transcription.

The Drosophila E74 gene is one of a small set of genes induced directly by the steroid hormone ecdysone at the onset of metamorphosis. Both in vitro and in vivo transcription assays have been used to delineate the promoter for the 6-kb E74 mRNA. Sequences upstream from position -83 had little effect on the amount of RNA synthesized in vitro, using extracts prepared from Drosophila Kc tissue culture cells. Deletion of a 5'-flanking TATA consensus sequence had no effect on the accuracy of transcriptional initiation and resulted in an increase in RNA synthesis, suggesting removal of a repressor binding site. Surprisingly, removal of the first two nucleotides of the transcribed region still allowed relatively high levels of transcription from the correct start site position. Removal of five additional nucleotides inactivated the promoter. In vitro transcription of a series of 3' deletions defined the 3' in vitro promoter boundary at position +43. Additional 5'-flanking sequences, between -181 and -83, were found to be necessary for efficient transcription in transfected Kc tissue culture cells. Two transcription factors that interact with the E74 promoter, zeste and GAGA, were studied in DNA-binding assays. zeste binds to two sites within the E74 promoter. These sites overlap with three of the six GAGA-binding sites. The zeste- and GAGA-binding sites lie within domains identified by deletion mapping as cis-acting transcriptional control elements.

Animals↗