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At least 91 records · Page 5Linked to original sources
PubMed1993

Molecular cloning of a novel mRNA sequence expressed in cleavage stage mouse embryos.

In an approach to study genes transcribed during early mouse development, a cDNA library was constructed from poly(A) RNA isolated from the 8-cell morula. The cDNA library was differentially screened with labelled cDNA probes synthesized on poly(A) RNA isolated from the 8-cell morula or unfertilized eggs. Six clones which increased in abundance in the 8-cell morula were selected and further analyzed. Sequencing analyses showed that some of these clones corresponded to RNA transcripts from B1 and B2 repetitive sequences, as well as mRNA for cytochrome C oxidase I and NADH dehydrogenase III derived from the mitochondrial genome. One clone was not identical to any known sequences. The unidentified sequence (MO25) was found at low levels in the unfertilized egg, but increased at the 2-cell stage. The predicted amino acid sequence revealed that the MO25 gene may encode a Ca2+ binding protein.

Amino Acid Sequence↗
PubMed1998

Identification of olfactory receptor mRNA sequences from the rat olfactory bulb glomerular layer.

In situ hybridization has demonstrated mRNA for olfactory receptors (OR) in the axon terminals of olfactory receptor neurons. Neurons that express the same OR appear to send their axons to two stereotyped glomeruli in the olfactory bulb (OB). Based on these observations, we tested the feasibility of using RT-PCR to isolate and sequence OR mRNA from small samples of the rat OB glomerular layer. Biomagnetic mRNA isolation followed by RT-PCR yielded partial sequences for 21 novel members of the OR family. The results suggest that the topography of OR mRNA can be mapped across the OB, to study synaptic specificity and odor representation in the olfactory system.

Animals↗
PubMed1989

Complete thrombospondin mRNA sequence includes potential regulatory sites in the 3' untranslated region.

The nucleotide sequence of human thrombospondin (TS) mRNA has been determined from human fibroblast and endothelial cDNAs. The sequence of 5802 bp begins 110 bp upstream from the initiator codon and includes the entire 3' untranslated region (UTR) of the mRNA. The coding region (3510 bp) specifies a protein of 1170 amino acids with all of the known features of the TS subunit (Frazier, W. A. 1987. J. Cell Biol. 105:625-632). The long 3' UTR of 2166 nucleotides is extremely A/T-rich, particularly in the latter half. It contains 37 TATT or ATTT(A) sequences that have been suggested as mediators of the stability of mRNAs for cytokines, lymphokines, and oncogenes (Shaw, G., and R. Kamen. 1986. Cell. 46:659-667). Another unusual feature of the 3' UTR of TS mRNA is a stretch of 42 nucleotides of which 40 are thymidines (uridine in the mRNA) including an uninterrupted sequence of 26 thymidines. This region is flanked by two sets of direct repeats suggesting that it may be an insertion element of retrotranscriptional origin. Comparison of the 3' untranslated region of TS mRNA with the GenBank data base indicates the greatest degree of similarity with an alpha-interferon gene which contains a number of the TATT/ATTT consensus sites. The degree of similarity between the TS and interferon sequences is the same in regions of the interferon gene corresponding to its coding and noncoding regions suggesting that most of the TS 3' UTR may be derived from an interferon gene or pseudogene. The features of the TS mRNA 3' UTR provide a potential explanation for the rapid regulation of TS message observed in cultured cells in response to PDGF and suggest that TS is a member of a group of proteins which are intimately involved in the control of cell growth and differentiation.

Amino Acid Sequence↗
PubMed2004

Trans-splicing of a mutated glycosylasparaginase mRNA sequence by a group I ribozyme deficient in hydrolysis.

RNA reprogramming represents a new concept in correcting genetic defects at the RNA level. However, for the technique to be useful for therapy, the level of reprogramming must be appropriate. To improve the efficiency of group I ribozyme-mediated RNA reprogramming, when using the Tetrahymena ribozyme, regions complementary to the target RNA have previously been extended in length and accessible sites in the target RNAs have been identified. As an alternative to the Tetrahymena model ribozyme, the DiGIR2 group I ribozyme, derived from a mobile group I intron in rDNA of the myxomycete Didymium iridis, represents a new and attractive tool in RNA reprogramming. We reported recently that the deletion of a structural element within the P9 domain of DiGIR2 turns off hydrolysis at the 3' splice site (side reaction) without affecting self-splicing [Haugen, P., Andreassen, M., Birgisdottir, A.B. & Johansen, S.D. (2004) Eur. J. Biochem. 271, 1015-1024]. Here we analyze the potential of the modified ribozyme, deficient in hydrolysis at the 3' splice site, for application in group I ribozyme-mediated trans-splicing of RNA. The improved ribozyme catalyses both cis-splicing and trans-splicing in vitro of a human glycosylasparaginase mRNA sequence with the same efficiency as the original DiGIR2 ribozyme, but without detectable levels of the unwanted hydrolysis.

Aspartylglucosylaminase↗
PubMed1996

Zebrafish translation elongation factor EF1 alpha mRNA: sequence and secondary structures.

We have determined the complete sequence of the translation elongation factor EF1 subunit alpha (EF1 alpha) mRNA of zebrafish, and the 3'-untranslated sequence of EF1 alpha mRNA of halibut. The 5'-untranslated leader sequence of the EF1 alpha mRNA starts with a polypyrimidine tract. This feature is shared with the mRNAs for ribosomal proteins, where it affects the utilization of mRNA by ribosomes. However, the secondary structures of these leader sequences may differ. 5'-Polypyrimidine tracts of vertebrate EF1 alpha mRNAs participate in the formation of stable stem-loop structures, whereas those of 15 randomly chosen mRNAs for ribosomal proteins do not. This difference may provide a basis for differential control of translation for the two classes of mRNA. The 3'-untranslated sequences of vertebrate EF1 alpha mRNA have diverged little during evolution. Analyses of sequence and putative secondary structures suggest that both sequence-specific interactions and secondary structures may have contributed to sequence conservation.

Amino Acid Sequence↗
PubMed2000

The genomic organization, complete mRNA sequence, cloning, and expression of a novel human intracellular membrane-associated calcium-independent phospholipase A(2).

During the sequencing of the long arm of chromosome 7 in the Human Genome Project, a predicted protein product of 40 kDa was identified, which contained two approximately 10-amino acid segments homologous to the ATP and lipase consensus sequences present in the founding members of a family of calcium-independent phospholipases A(2). Detailed inspection of the identified sequence (residues 79, 671-109,912 GenBank accession no. AC005058) demonstrated that it represented only a partial sequence of a larger undefined polypeptide product. Accordingly, we identified the complete genomic organization of this putative phospholipase A(2) through analyses of previously published expressed sequence tags, PCR of human heart cDNA, and 5'-rapid amplification of cDNA ends. Polymerase chain reaction and Northern blotting demonstrated a 3.4-kilobase message, which encoded a polypeptide with a maximum calculated molecular weight of 88476.9. This 3.4-kilobase message was present in multiple human parenchymal tissues including heart, skeletal muscle, placenta, brain, liver, and pancreas. Cloning and expression of the protein encoded by this message in Sf9 cells resulted in the production of two proteins of apparent molecular masses of 77 and 63 kDa as assessed by Western analyses utilizing immunoaffinity-purified antibody. Membranes from Sf9 cells expressing recombinant protein released fatty acid from sn-2-radiolabeled phosphatidylcholine and plasmenylcholine up to 10-fold more rapidly than controls. The initial rate of fatty acid release from the membrane fraction was 0. 3 nmol/mg.min. The recombinant protein was entirely calcium-independent, had a pH optimum of 8.0, was inhibited by (E)-6-(bromomethylene)-3-(1-naphthalenyl)-2H-tetrahydropyran-2-one (IC(50) = 3 microM), and was predominantly present in the membrane-associated fraction. Collectively, these results describe the genomic organization, complete mRNA sequence, and sn-2-lipase activity of a novel intracellular calcium-independent membrane-associated phospholipase A(2).

Amino Acid Sequence↗
PubMed1994

A new variant Cu/Zn superoxide dismutase (Val7-->Glu) deduced from lymphocyte mRNA sequences from Japanese patients with familial amyotrophic lateral sclerosis.

We have identified a new mutant Cu/Zn superoxide dismutase (SOD1) deduced from the nucleotide sequences of peripheral blood lymphocyte mRNA from Japanese patients with familial amyotrophic lateral sclerosis (FALS). Sequence analysis of reverse transcriptase-initiated PCR amplified mRNA revealed a heterozygosity indicative of one normal allele and one variant allele with a T-->A transversion. This base change led to replacement of valine by glutamic acid at position 7 of 153-residue SOD1 molecule, and produced a new restriction site for Alu I in the exon 1. Restriction fragment length polymorphism analysis confirmed the linkage of this mutation with this type of FALS. Both enzymatic activity and protein of the SOD1 were reduced in red blood cells from the patient.

Adult↗
PubMed1989

The mumps virus nucleocapsid mRNA sequence and homology among the Paramyxoviridae proteins.

The nucleotide sequence of mumps virus nucleocapsid protein (NP) mRNA has been determined from two overlapping cDNA clones and confirmed by partial sequencing of the mRNA and the genome. The mRNA contains 1844 nucleotides excluding poly(A) and encodes a protein of 553 amino acids with a calculated molecular weight of 61,792. A comparison of the mumps virus nucleocapsid protein sequence with that of other paramyxoviruses revealed a moderate degree of homology (33.1%) with the Newcastle disease virus (NDV) only. The nucleocapsid proteins of all paramyxoviruses studied to date, excluding that of the genus pneumovirus, have a conserved sequence of six amino acids (Ser-Tyr-Ala-Met-Gly-Val) except that of NDV which has a mismatch of two amino acids (Ser-Phe-Ala-Met-Gly-Met) in that sequence. In addition, there is another conserved region of seven amino acids (Phe-Ala-Pro-Gly-X-Tyr-Pro) in the nucleocapsid proteins of mumps virus, Sendai virus and parainfluenza virus type 3. The nucleocapsid proteins of measles virus and canine distemper virus (CDV) also have this conserved region but with three conservative amino acid changes.

Amino Acid Sequence↗
PubMed1998

Long-range base pairing in Drosophila and human mRNA sequences.

The potential for long-range base pairing between the 5' and 3' ends of mRNA molecules was examined for 134 Drosophila and 204 human sequences collected from the GenBank database. Each sequence was divided into two parts, a 5' sequence taken from the start of the protein-encoding region and a 3' sequence taken from the end of the transcript. The strongest RNA pairing stem between each pair of 5' and 3' sequences was identified and scored using an alignment program modified to incorporate RNA base pairing. The observed pairing scores were then compared with a random distribution of scores generated by aligning each 5' sequence to random permutations of its corresponding 3' sequence. For both the Drosophila and the human mRNAs, the observed pairing scores were significantly biased toward the upper tail of the random distributions, with 61% of the Drosophila sequences and 64% of the human sequences falling within the upper half of the random distributions. This suggests that a pattern of long-range base pairing may be a common feature of eukaryotic mRNAs. We have also analyzed a subset of Drosophila and human mRNAs which show the greatest potential for long-range pairing. The human pairings appear to be stronger and localized to more specific regions near the ends of the mRNA sequence than those of Drosophila.

Animals↗
PubMed1985

Tangier disease. The complete mRNA sequence encoding for preproapo-A-I.

A cDNA library of Tangier liver mRNA has been established, and two apo-A-I-containing clones were identified. The complete derived amino acid sequence of preproapo-A-I has been established by nucleic acid sequence analysis of cloned apo-A-I cDNA and specific primer extensions on Tangier liver RNA. Sequence analysis of the longest cDNA clone, pMDB136T, established the derived amino acid sequence of residues 116-243 of plasma apo-A-I. The remaining portion of the sequence of Tangier preproapo-A-I mRNA was established by sequence analysis of specific primer extensions of synthetic oligonucleotides on Tangier liver mRNA. This latter technique provided the derived amino acid sequence of residues -24 to 116, thus completing the entire preproapo-A-I structure. The structure of Tangier preproapo-A-I was identical to normal preproapo-A-I except for a single base substitution (G----T) which resulted in the isosteric replacement of a glutamic acid residue at position 120 to aspartic acid. These results are interpreted as indicating that there is no major structural defect in Tangier apo-A-I, and the rapid rate of catabolism of apo-A-I in Tangier disease is due to a post-translational defect in apo-A-I metabolism.

Amino Acid Sequence↗
PubMed1986

Primary structure of the human melanoma-associated antigen p97 (melanotransferrin) deduced from the mRNA sequence.

p97 is a cell-surface glycoprotein that is present in most human melanomas but only in trace amounts in normal adult tissues. To determine the structure of this tumor-associated antigen and to identify its functional domains, we have purified and cloned p97 mRNA and determined its nucleotide sequence. The mRNA encodes a 738-residue precursor, which contains the previously determined N-terminal amino acid sequence of p97. After removal of a 19-residue signal peptide, the mature p97 molecule comprises extracellular domains of 342 and 352 residues and a C-terminal 25-residue stretch of predominantly uncharged and hydrophobic amino acids, which we believe acts as a membrane anchor. Each extracellular domain contains 14 cysteine residues, which form seven intradomain disulfide bridges, and one or two potential N-glycosylation sites. Protease digestion studies show that the three major antigenic determinants of p97 are present on the N-terminal domain. The domains are strikingly homologous to each other (46% amino acid sequence homology) and to the corresponding domains of human serum transferrin (39% homology). Conservation of disulfide bridges and of amino acids thought to compose the iron binding pockets suggests that p97 is also related to transferrin in tertiary structure and function. We propose that p97 be renamed melanotransferrin to denote its original identification in melanoma cells and its evolutionary relationship to serotransferrin and lactotransferrin, the other members of the transferrin superfamily.

Amino Acid Sequence↗
PubMedDate not supplied

mRNA sequence for human cardiodilatin-atrial natriuretic factor precursor and regulation of precursor mRNA in rat atria.

The mammalian cardiac atrium has recently been shown to contain numerous peptides that exert marked effects on kidney function and vascular resistance. With one exception, the peptides have potent natriuretic and diuretic activities, and sequence similarities suggest that they may be derived from a common atrial natriuretic factor (ANF) precursor. The exception, cardiodilatin (CDD), differs from the ANF peptides in possessing potent vasorelaxant activity, but not natriuretic and diuretic activities. Here we report the cloning and sequence analysis of the cDNA for the human precursor protein (preproCDD-ANF) containing both the CDD and ANF sequences. The CDD sequence represents the N-terminal sequence preceded directly by a signal peptide, while the ANF sequence is present at the C-terminal end of the protein. Using hybridization analysis, we further show that the amount of rat preproCDD-ANF mRNA, which is synthesized selectively in the atria but not the ventricles, markedly decreases on water deprivation, suggesting that the water-electrolyte balance may be an important factor in the regulation of the expression of the preproCDD-ANF gene.

Amino Acid Sequence↗
PubMed1990

Definition of the complete Schistosoma mansoni hemoglobinase mRNA sequence and gene expression in developing parasites.

Schistosoma mansoni uses a variety of proteases termed hemoglobinases to obtain nutrition from host globin. Previous reports have characterized cDNAs encoding 1 of these enzymes. However, these sequences did not define the primary structures of the mRNA and protein. The complete sequence of the 1390 base mRNA has now been determined. It encodes a 50 kDa primary translation product. In vitro translations coupled with immunoprecipitations and Western blots of parasite lysates allowed visualization of the 50 kDa form. Production of the 31 kDa mature hemoglobinase from the 50 kDa species involves removal of both NH2 and COOH terminal residues from the primary translation product. Expression of hemoglobinase mRNA and protein was examined during larval parasite development. Low levels were observed in young schistosomula. After 6-9 days in culture, high hemoglobinase levels were seen which correlated with the onset of red blood cell feeding. Immunoelectron microscopy was employed to examine hemoglobinase location and function. In adult worms the enzyme was associated with the gut lumen and gut epithelium. In cercariae, the protease was observed in the head gland, suggesting new roles for the protease.

Amino Acid Sequence↗
PubMed1977

The extensive homology between mRNA sequences of normal and SV40-transformed human fibroblasts.

The poly(A)-containing messenger RNA of normal diploid fibroblast and SV40-transformed progeny cells are compared by cross-hybridizing cDNA. We find a high degree of homology between the mRNA from normal and transformed cells. Despite imperfections in the procedure, the technique permits the conclusion that, at most, 3% of the mRNA in the transformed cell has sequences not present in the normal parental cell. Furthermore, much of the difference appears to occur in low and intermediate complexity classes of mRNA molecules. Extension homology in the mRNA sequences of disparate cell lines may be a general phenomenon, and even HeLa cell mRNA is nearly identical to that of diploid human fibroblasts.

Base Sequence↗
PubMed2005

mRNA sequence features that contribute to translational regulation in Arabidopsis.

DNA microarrays were used to evaluate the regulation of the proportion of individual mRNA species in polysomal complexes in leaves of Arabidopsis thaliana under control growth conditions and following a mild dehydration stress (DS). The analysis determined that the percentage of an individual gene transcript in polysomes (ribosome loading) ranged from over 95 to <5%. DS caused a decrease in ribosome loading from 82 to 72%, with maintained polysome association for over 60% of the mRNAs with an increased abundance. To identify sequence features responsible for translational regulation, ribosome loading values and features of full-length mRNA sequences were compared. mRNAs with extreme length or high GU content in the 5'-untranslated regions (5'-UTRs) were generally poorly translated. Under DS, mRNAs with both a high GC content in the 5'-UTR and long open reading frame showed a significant impairment in ribosome loading. Evaluation of initiation A+1UG codon context revealed distinctions in the frequency of adenine in nucleotides -10 to -1 (especially at -4 and -3) in mRNAs with different ribosome loading values. Notably, the mRNA features that contribute to translational regulation could not fully explain the variation in ribosome loading, indicating that additional factors contribute to translational regulation in Arabidopsis.

3' Untranslated Regions↗
PubMed1978

Complex population of mRNA sequences in large polyadenylylated nuclear RNA molecules.

Polyadenylylated heterogeneous nuclear RNA [poly(A)-hnRNA] from mouse brain was subjected to electrophoresis in agarose gels containing CH3HgOH, and molecules larger than 8 kilobases or 13 kilobases were recovered. cDNA was then transcribed from polyadenylylated RNA fragments cleaved from these large molecules. The resulting cDNA hybridized almost to completion with poly(A)-mRNA isolated from mouse brain polysomes. From the hybridization kinetics of this cDNA with its template RNA, it was estimated that the sequence complexity of the 3'-proximal sequences (of the same average size as mRNA) of the greater than 8 kilobase poly(A)-hnRNA was about 57,000 kilobases. The sequence complexity of poly(A)-mRNA, estimated from the template-driven hybridization kinetics of its respective cDNA, was about 110,000 kilobases. It is concluded that most, if not all, of the 3'-proximal sequences of large poly(A)-hnRNA molecules are homologous with mRNA in the mouse brain and that at least 40,000 different mRNA sequences (or portions of mRNA sequences) are represented in the 3'-proximal sequences of greater than 8 kilobase poly(A)-hnRNA.

Animals↗
PubMed1987

(A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences.

Several 3' splice signals in nuclear precursor mRNAs have already been known for some time: the AG doublet on the left-hand side of the splice and a run of pyrimidines just upstream of it. More recently it has been noted that the YNYTRAY sequence (where Y is a pyrimidine, R a purine and N any base) is a branching-sequence participating in formation of a lariat structure. Keller and Noon have shown the existence of several putative consensus sequences at this site. In this work, extensive computations of the distributions of 256 quartets in all primate nuclear pre-mRNA intron sequences present in GenBank have been carried out. Several putative signals upstream and downstream of the 3' splice have been detected. These have been compared with the results obtained in analogous computations carried out on all nuclear pre-mRNA introns present in a combined eukaryotic file containing mammal, non-mammalian vertebrate, invertebrate and plant sequences. The distributions of the more interesting oligomers are shown here. Of particular interest are the putative (A)GGG(A) signal 60 nucleotides upstream of the 3' splice site and (A)CCC(A) 3-40 nucleotides downstream of it. A possible splicing model explaining these data and involving formation of alternative hairpin loop structures is proposed.

Animals↗