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PubMed1980

Messenger RNA for alpha 2u-globulin of rat liver. Purification, partial characterization of the mRNA, and synthesis of a Hae III restriction fragment as its cDNA probe.

The mRNA for the androgen-dependent hepatic protein, alpha 2u-globulin is normally present in the liver of mature male rats to the extent of about 1% of the total mRNA population. alpha 2u mRNA which was found to migrate as a 14 S band was purified about 18-fold through preparative urea-agarose gel electrophoresis. 32P-Labeled cDNA synthesized with this partially purified alpha 2u mRNA was used as substrate for two restriction endonucleases Hha I and Hae III. Digestion of the cDNA with Hha I failed to reduce its electrophoretic heterogeneity. However, Hae III digestion of the cDNA preparation greatly reduced the molecular complexity and produced several distinct cDNA bands. One of these Hae III fragments (Band A) containing 410 nucleotide residues was extracted from polyacrylamide gel and found to be complementary to alpha 2u mRNA. The identity of this cDNA fragment was established by its ability to inhibit selectively the translation of alpha 2u mRNA in the rabbit reticulocyte cell-free system and by its hybridization kinetics with poly(A)+ hepatic RNA from animals with different rates of alpha 2u synthesis. The relative R0t 1/2 values showed a direct correlation between mRNA sequences complementary to the cDNA fragment (A) and to both translatable alpha 2u mRNA and hepatic level of alpha 2u-globulin in adult male, female, and maturing male rats. Thus, the cDNA fragment containing 410 nucleotide residues generated by the restriction cleavage with Hae III can be used as a convenient probe for identification and quantitation of alpha 2u mRNA under different physiological and experimental conditions.

Alpha-Globulins↗
PubMed1978

Absence of beta mRNA in beta0-thalassemia in Kurdish Jews.

We report the characterization of the amount of beta mRNA in a Kurdish Jewish population with beta0-thalassemia using the same methods employed for characterization of the Catania and Ferrara beta0 patients. We found very low amounts of beta mRNA sequences, consistent with the presence of beta0-thalassemia of the beta mRNA-negative population type. In addition, no globin gene deletion was detected that could account for the absence of beta mRNA.

Adolescent↗
PubMed2001

Cloning and expression of a ferritin subunit for Galleria mellonella.

Ferritin was purified from iron-fed Galleria mellonella hemolymph by ultra centrifugation and FPLC (Superose 6). SDS-PAGE revealed three bands of 26, 30, and 32 kDa. The ferritin 26 kDa subunit cDNA was obtained from RT-PCR using primer designed from N-terminal sequence analysis. 5'-RACE was used to obtain the complete protein coding sequence. The sequence encodes a 211 amino acid polypeptide including a 20 amino acid leader peptide. An IRE (iron-responsive element) sequence with a predicted stem-loop structure was present in the 5'-UTR of ferritin mRNA. Sequence alignment has a sequence identity with Calpodes ethlius (S)(74%), Drosophila melanogaster (50%), and Aedes aegypti (39%). Northern blot analysis indicated that there were 1.5- and 1.75-fold increases in the expression of ferritin mRNA after iron-fed fat body and midgut, respectively. Also, we confirmed that the ferritin mRNA is not expressed in adult ovary and testis. Arch.

Amino Acid Sequence↗
PubMed1997

Extensive RNA editing and possible double-stranded structures determining editing sites in the atpB transcripts of hornwort chloroplasts.

Three nonsense codons and an unusual initiation codon were located within the putative coding region of the atpB gene of chloroplast DNA of the hornwort Anthoceros formosae. Nucleotide sequencing of cDNA prepared from transcripts revealed extensive RNA editing. The unusual initiation codon ACG was changed to AUG and three nonsense codons were converted into sense codons. In total 15 C residues of the genomic DNA were replaced by U residues in the mRNA sequences, while 14 U residues were replaced by C residues. This is the highest number of editing events for a chloroplast mRNA reported so far. Partial editing was also shown in a cDNA clone where 23 sites were edited but six sites remained unedited, representing the existence of premature mRNA. The expected two-dimensional structure of the mRNA shows the existence of a sequence complementary to every editing site, which can produce continuous base pairing longer than 5 bp, suggesting that mispairing in the double strand is the site determinant for RNA editing in Anthoceros chloroplasts. Comparison of the cDNA sequence with other chloroplast genes suggests that the mechanism arose in the first land plants and has been reduced during evolution.

Amino Acid Sequence↗
PubMed1992

Complete complementary DNA sequence of the third component of complement of lamprey. Implication for the evolution of thioester containing proteins.

Lamprey liver mRNA sequences were amplified by reverse transcriptase-polymerase chain reaction using primers synthesized according to the amino acid sequences at the thioester region common to the mammalian C3, C4, and alpha 2-macroglobulin (alpha 2M). Two different cDNA species were identified that showed a close similarity to the mammalian C3 or alpha 2M sequences, respectively. Using the C3-like sequence as a probe, two overlapping cDNA clones were isolated from the lambda ZAP library, which together covered the entire region encoding the putative lamprey pro-C3. The deduced amino acid sequence of the putative lamprey pro-C3 contained 1660 amino acids and showed 31%, 22%, 23%, and 16% amino acid sequence identity with mouse C3, C4, C5, and human alpha 2M, respectively. The distributions of cysteine residues were completely identical between the mouse C3 and the putative lamprey C3 except that the lamprey sequence had two additional cysteine residues in the alpha-chain. The possible beta-alpha and alpha-gamma processing sites were found at exactly the same positions as in mammalian C4. These results suggest that the putative lamprey C3 retains a close similarity to the common ancestor of the mammalian C3 and C4, which appeared to have had a three-subunit chain structure.

Amino Acid Sequence↗
PubMed1994

Sequence analysis and compositional properties of untranslated regions of human mRNAs.

A detailed computer analysis of the untranslated regions, 5'-UTR and 3'-UTR, of human mRNA sequences is reported. The compositional properties of these regions, compared with those of the corresponding coding regions, indicate that 5'-UTR and 3'-UTR are less affected by the isochore compartmentalization than the corresponding third codon positions of mRNAs. The presence of higher functional constraints in 5'-UTR is also reported. Dinucleotide analysis shows a depletion of CpG and TpA in both sequences. A search for significant sequence motifs using the WORDUP algorithm reveals the patterns already known to have a functional role in the mRNA UTR, and several other motifs whose functional roles remain to be demonstrated. This type of analysis may be particularly useful for guiding site-directed mutagenesis experiments. In addition, it can be used for assessing the nature of anonymous sequences now produced in large amounts in megabase sequencing projects.

Algorithms↗
PubMed2003

[Study of hemin-induced gene expression in K562 cells].

OBJECTIVE: To identify hemin-induced gene expression in K562 cells. METHODS: Poly A(+) RNAs were isolated from hemin-induced (tester) and non-induced K562 cells (driver) respectively, and double-strand cDNAs were synthesized by reverse transcription. The forward subtracted cDNA library was constructed by using suppression subtractive hybridization (SSH) techniques. The recombinant plasmids were extracted and the positive clones were identified by EcoR I digestion after the amplification and screening of the library. The inserts were amplified by PCR. The upregulated cDNA transcripts were identified by reverse dot blot hybridization, DNA sequencing and homology analysis with GenBank database "blast" respectively. RESULTS: Fifteen upregulated clones were identified and most of them were homologous to the mRNA sequences of protein with known function, including globin epsilon1, glutathione S-transferase like glutathione transferase Omega (GSTTLp28), selenoprotein X1 (SEPX1), triosephosphate isomerase (TPI1), ribosomal protein L7 (RPL7), ribosomal protein S13 (RPS13), ferritin light polypeptide, globin A gamma, RAD 51 homolog C(RAD51C), ferritin heavy polypeptide, X-box binding protein (XBP1). A part of the hemin-induced cDNA clones exhibited sequence similarities to that of the GenBank registered mRNA with unknown function of their expressed proteins, including the cDNA clones of DKFZp434I116, hypothetical protein HSPC014 and NOL1R2 proteins. CONCLUSIONS: Hemin mainly induces the genes expression related to erythroid differentiation, protein synthesis and metabolism in K562 cell. There results provide comprehensive information useful for the differential gene expression in hemin-induced erythroid differentiation and for further function study of genes involved in hematopoiesis.

Blotting, Northern↗
PubMed1976

Further studies on collagen mRNA: partial chemical characterization and polyadenylic acid sequence.

Collagen mRNA has already been purified and characterized by us. Its purity has now been enhanced by two different methods. Gel electrophoresis shows in either method, a single peak with the same mobility already reported: 1.05 X 10(6) daltons. Base composition analyses of collagen mRNA purified by either method were almost identical. Chemical analyses of the isolated polyadenylic acid stretch show that it is, 0.48 X 10(5) daltons-long, (about 140 nucleotides-long), contains 75% AMP, and is located at the 3' end of the polymer.

Animals↗
PubMed1994

Cloning of a cDNA for the FAD-linked glycerol-3-phosphate dehydrogenase from rat liver and its regulation by thyroid hormones.

A full-length 2.4-kb cDNA for the FAD-linked glycerol-3-phosphate dehydrogenase (EC 1.1.99.5) was cloned from rat liver using PCR techniques. The cloned gene encodes a protein of 727 amino acids. The calculated molecular mass of 80,898 Da is higher than the apparent molecular mass observed by SDS/PAGE (74,000 Da) of the purified enzyme. This result indicates that the enzyme is synthesized as a precursor with a putative mitochondrial signal sequence. mRNA for this gene was detected in liver, heart, muscle, brain, testes, and pancreas. With the exception of testes, basal expression levels were very low in all tissues examined. However, application of thyroid hormones led to a 10- to 15-fold increase in liver glycerol-3-phosphate dehydrogenase mRNA, whereas hypothyroidism further decreased the mRNA level.

Amino Acid Sequence↗
PubMed1990

Heterogeneity of mRNA and protein products arising from the protein 4.1 gene in erythroid and nonerythroid tissues.

Immunologically cross-reactive isoforms of the cytoskeletal element protein 4.1 have been identified in many tissues in which they exhibit heterogeneity of molecular weight, abundance, and intracellular localization. To examine the basis for isoform production in erythroid and nonerythroid tissues, we have compared the structure and expression of cDNAs isolated from human erythroid and nonerythroid sources. We have encountered cDNAs representing many distinct mRNA sequences. These exhibit complete nucleotide sequence homology along most of their lengths. Differences were confined to five sequence blocks designated Motifs I-V, which were present or absent in each mRNA moiety. Motif I was expressed only in erythroid cells; it encodes 21 amino acids in a well-characterized spectrin/actin binding domain. Motif II, located near the COOH terminus of the 80-kD "erythroid" protein 4.1 molecule is present in the vast majority of transcripts from both erythroid and nonerythroid cells. Motifs IV and V alter the 5' untranslated region: simultaneous insertion of Motif IV and deletion of Motif V in the untranslated region inserts a new initiator methionine and establishes a contiguous open reading frame encoding a novel 135-kD protein 4.1 molecule. By immunochemical analysis we have identified the longer isoform in cells. Our results are most consistent with tissue-specific alternative mRNA splicing of transcripts of the protein 4.1 gene to yield numerous isoforms. These isoforms exhibit tissue specificity and alter strategic portions of the molecule. Moreover, we describe a novel high molecular weight form of protein 4.1 that arises by splicing events which allow translation at an upstream site.

Amino Acid Sequence↗
PubMed1995

Gs couples thyrotropin-releasing hormone receptors expressed in Xenopus oocytes to phospholipase C.

Coupling of thyrotropin-releasing hormone (TRH) receptors to individual G-proteins has been studied in Xenopus oocytes injected with receptor cRNA and antisense oligonucleotides to mRNA encoding different G-protein alpha- and beta-subunits. Injection of antisenses which target mRNA sequences shared by several G-protein alpha or beta gamma polypeptides effectively blocked Ca(2+)-dependent Cl- currents induced by TRH through activation of phospholipase C. Three different alpha s-specific antisense oligonucleotides complementary to sequences located in different positions along the coding region of the alpha s protein mRNA were highly effective in inhibiting TRH-induced responses. Anti-alpha o, -alpha q, -alpha i, or -alpha z oligonucleotides were not able to modify the TRH-evoked response. In contrast, anti-alpha o, but not anti-alpha s, oligonucleotides blocked the response to serotonin in oocytes injected with serotonin 5-HT1c receptor cRNA. Cholera toxin catalyzed the [32P]ADP-ribosylation of 40-42- and 50-52-kDa proteins in GH3 cell plasma membranes. [32P]ADP-ribosylation of oocyte membranes with the toxin labeled several proteins. These include a single 50-55-kDa substrate, which is clearly diminished in membranes from anti-alpha s-injected oocytes. Amplification of oocyte RNA in a polymerase chain reaction system and sequencing of the amplified products demonstrated that anti-alpha s oligonucleotides selectively recognize the message for the Xenopus alpha s polypeptide. It is concluded that Gs, but not Go, Gq, Gi, or Gz, couples TRH receptors expressed in oocytes to activation of phospholipase C and subsequent inositol 1,4,5-trisphosphate-dependent stimulation of Ca(2+)-dependent Cl- currents.

Animals↗
PubMed1992

Gene expression in cotton (Gossypium hirsutum L.) fiber: cloning of the mRNAs.

Cotton, an important natural fiber, is a differentiated epidermal cell. The number of genes that are active in fiber cells is similar to those in leaf, ovule, or root tissues. Through differential screening of a fiber cDNA library, we isolated five cDNA clones that are preferentially expressed in fiber. One of the cDNA clones, pCKE6, corresponded to an abundant mRNA in fiber. Transcripts for E6 were detected throughout the development of the fiber. Immunoprecipitation of in vitro translation products and Western blot analysis of fiber proteins showed two polypeptides in the range of 30-32 kDa as the products of E6 mRNA. Sequence analysis and hybrid-selected RNA translation also suggest that E6 mRNAs encode two polypeptides. Concentrations of E6 mRNA and protein are highest during the late primary cell wall and early secondary cell wall synthesis stages. Sequence comparison of E6 with other known eukaryotic and prokaryotic genes reveals no significant homology (GenBank; December 1991). E6 or a homologous gene(s) is conserved in several members of Malvaceae as well as in one other fiber-producing plant, kapok, but is not found in several other plants examined or in Acetobacter xylinum. A genomic clone corresponding to pCKE6 was isolated, and the promoter element of the E6 gene was shown to direct the expression of a carrot extensin mRNA in a tissue-specific and developmentally regulated fashion in transgenic cotton plants.

Amino Acid Sequence↗
PubMed1992

Transgenic mice expressing full-length human apolipoprotein B-100. Full-length human apolipoprotein B mRNA is essentially not edited in mouse intestine or liver.

Apolipoprotein (apo) B-100 mRNA is edited in the small intestine (in all mammals examined) and the liver (in mice and rats only) to produce apoB-48 mRNA. ApoB mRNA editing involves a C-->U conversion of the first base of the codon CAA for Gln-2153 in apoB-100, changing it to an in-frame stop codon (UAA). The edited mRNA encodes apoB-48, which is colinear with the N-terminal 48% of apoB-100. ApoB mRNA editing can be reproduced in vitro using cellular extracts from one species to edit synthetic apoB mRNA sequences from a different species. Editing of transcripts from transfected genes also appears not to be species-specific. We have produced transgenic mice that express full-length human apoB-100 mRNA at high levels in the liver and small intestine. Human apoB-100 (a 550-kDa protein) but not apoB-48 (a 260-kDa protein) is detected in total plasma (at approximately 22 mg/dl) and in very low density and low density lipoproteins. The endogenous mouse plasma apoB concentration is reduced by approximately 45% in the transgenic animals. Thus, the transgenic mice form an animal model for familial hyperapolipoprotein B, an inherited form of hyperlipidemia. To our surprise, we found that the full-length human apoB mRNA consists of > 99% apoB-100 mRNA in both the liver and small intestine; < 1% of edited (apoB-48) mRNA was detected. The proportions of endogenous mouse apoB-48 (edited) mRNA (60 and 90% in the liver and small intestine, respectively) were identical in transgenic mice and their nontransgenic littermates. Therefore, full-length human apoB mRNA is resistant to editing by the mouse editing enzyme in vivo; the unchanged proportion of endogenous mouse apoB-48 mRNA in the transgenic mice suggests that the human mRNA competes poorly with the mouse sequence for interacting with the editing enzyme. This observation has implications for the sequence specificity and mechanism of RNA editing. Furthermore, we should exercise caution in the interpretation of in vitro RNA-editing experiments.

Animals↗
PubMed1992

Importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Escherichia coli.

The trmD operon of Escherichia coli consists of the genes for the ribosomal protein (r-protein) S16, a 21 kilodalton protein (21K) of unknown function, the tRNA(m1G37)methyltransferase (TrmD), and r-protein L19, in that order. The synthesis of the 21K and TrmD proteins is 12 and 40-fold lower, respectively, than that of the two r-proteins, although the corresponding parts of the mRNA are equally abundant. This translational control of expression of at least the 21K protein gene (21K), is mediated by a negative control element located between codons 18 and 50 of 21K. Here, we present evidence for a model in which mRNA sequences up to around 100 nucleotides downstream from the start codon of 21K fold back and base-pair to the 21K translation initiation region, thereby decreasing the translation initiation frequency. Mutations in the internal negative control element of 21K that would prevent the formation of the proposed mRNA secondary structure over both the Shine-Dalgarno (SD) sequence and the start codon increased expression up to about 20-fold, whereas mutations that would disrupt the base-pairing with the SD-sequence had only relatively small effects on expression. In addition, the expression increased 12-fold when the stop codon of the preceding gene, rpsP, was moved next to the SD-sequence of 21K allowing the ribosomes to unfold the postulated mRNA secondary structure. The expression increased up to 150-fold when that stop codon change was combined with the internal negative control element base-substitutions that derepressed translation about 20-fold. The negative control element of 21K does not seem to be responsible for the low expression of the trmD gene located downstream. However, a similar negative control element native to trmD can explain at least partly the low expression of trmD. Possibly, the two mRNA secondary structures function to decouple translation of 21K and trmD from that of the respective upstream cistron in order to achieve their independent regulation.

Base Sequence↗
PubMed1982

Differing responses of globin and glycophorin gene expression to hemin in the human leukemia cell line K562.

The human leukemia cell line, K562, produces embryonic and fetal hemoglobins and glycophorin A, proteins normally associated only with erythroid cells. Hemoglobin accumulation is enhanced by exposure of the cells to 0.05 mM hemin. We have examined K562 cells before and after exposure to hemin to determine whether expression of these erythroid proteins was shared by all cells or confined to specific subpopulations. Globin gene expression was examined by quantitation of globin mRNA sequences, using a 3H-globin cDNA molecular hybridization probe. Constitutive cells produced globin mRNA, the content of which was increased 3-4-fold by hemin. Cell-to-cell distribution of globin mRNA was determined by in situ hybridization of 3H-globin cDNA to constitutive and hemin-treated K562 cells. Virtually all cells in the culture exhibited grain counts above background, indicating globin gene expression by all cells, rather than a confined subpopulation. Virtually all hemin-treated cells had 3-5-fold higher grain counts, indicating uniformly increased globin gene expression. The glycophorin content of K562 cells was estimated by fluorescence-activated cell sorting (FACS) of cells labeled with fluorescein-labeled antiglycophorin antiserum. The vast majority of constitutive cells contained glycophorin, but exhibited to apparent increase in glycophorin accumulation after hemin exposure. Thus, glycophorin and globin genes exhibited differential responses to hemin. These differences could reflect normal differences in the patterns of specialized gene expression in stem cells. Alternatively, different aberrations of gene expression could be occurring in response to the determinants of the neoplastic properties of K562.

Amino Acid Sequence↗
PubMed1992

Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids.

The NADH dehydrogenase subunit A (ndhA) gene from maize chloroplasts encodes a highly conserved peptide, which at several positions could be restored to consensus sequences by potential C-to-U editing of the codons involved. This gene was, therefore, chosen for analysis of its mRNA sequence in the form of amplified cDNA. A comparison of this cDNA sequence with the plastome-encoded ndhA sequence reveals four C-to-U editing sites, thereby demonstrating as a novel finding that chloroplast editing can also affect internal mRNA positions. All the edited codons restore amino acids that are conserved in the ndhA-encoded peptides of other chloroplast species. Alignment with homologous mitochondrial NADH-ubiquinone reductase subunit 1 (nad1) sequences of plant and even nonplant species shows that two of the editing positions restore universally conserved amino acids and that one editing site is even shared with nad1 mRNA of plant mitochondria. No editing sites could be detected in the cDNA derived from transcripts of the maize chloroplast RNA polymerase alpha-subunit (rpoA) gene.

Amino Acid Sequence↗
PubMed1992

Posttranscriptional control of glutathione S-transferase pi gene expression in human breast cancer cells.

The glutathione S-transferase pi gene (GST pi) is highly expressed in estrogen receptor negative (ER-) but not expressed in ER+ human breast cancer cell lines. To define regulatory mechanisms of GST pi gene expression, we analyzed both the activity of the GST pi promoter and the posttranscriptional fate of GST pi RNA sequences in three ER+ and three ER- breast cancer cell lines. Expression of a transiently transfected CAT reporter gene driven by the GST pi promoter and 2203 nucleotides of 5'-flanking sequences were similar in all six cell lines regardless of ER status. Endogenous GST pi transcription rates in nuclei isolated from ER- cells were quite low despite high steady state levels of cytoplasmic mRNA. Furthermore, the endogenous GST pi gene was transcribed in ER+ nuclei at rates similar to those obtained in ER- nuclei. We determined the stabilities of mRNAs transcribed from the endogenous GST pi gene (ER- cells) and from a stably transfected GST pi cDNA expression vector (ER+ and ER- cells). The endogenous GST pi mRNA was extraordinarily stable in ER- cells. Comparisons between transfected ER+ and ER- cells revealed no significant differences in the stabilities of transfection-derived GST pi mRNA sequences. We conclude that GST pi mRNA stability contributes significantly to the high levels of cytoplasmic mRNA observed in ER- cells, but that the differential expression of GST pi in ER+ versus ER- cells is governed by other posttranscriptional processes.

Breast Neoplasms↗
PubMed1999

The positive relationship between codon usage bias and translation initiation AUG context in Saccharomyces cerevisiae.

The relationship between the codon usage bias and the sequence context surrounding the AUG translation initiation codon was examined in 211 Saccharomyces cerevisiae mRNA sequences. The codon usage bias and the number of matches to optimal AUG context, (A/U)A(A/C)AA(A/C)AUGUC(U/C), for translation initiation showed a positive relationship, indicating that these two factors are evolutionally under the similar natural selection constraint at the translation level. A new index (AUGCAI = AUG Context Adaptation Index) for the measure of optimal AUG context was devised, and the importance of each position of AUG context was also examined.

Base Sequence↗