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At least 721 records · Page 40Linked to original sources
PubMed1991

cDNA and amino acid sequences of rainbow trout (Oncorhynchus mykiss) lysozymes and their implications for the evolution of lysozyme and lactalbumin.

The complete 129-amino-acid sequences of two rainbow trout lysozymes (I and II) isolated from kidney were established using protein chemistry microtechniques. The two sequences differ only at position 86, I having aspartic acid and II having alanine. A cDNA clone coding for rainbow trout lysozyme was isolated from a cDNA library made from liver mRNA. Sequencing of the cloned cDNA insert, which was 1 kb in length, revealed a 432-bp open reading frame encoding an amino-terminal peptide of 15 amino acids and a mature enzyme of 129 amino acids identical in sequence to II. Forms I and II from kidney and liver were also analyzed using enzymatic amplification via PCR and direct sequencing; both organs contain mRNA encoding the two lysozymes. Evolutionary trees relating DNA sequences coding for lysozymes c and alpha-lactalbumins provide evidence that the gene duplication giving rise to conventional vertebrate lysozymes c and to lactalbumin preceded the divergence of fishes and tetrapods about 400 Myr ago. Evolutionary analysis also suggests that amino acid replacements may have accumulated more slowly on the lineage leading to fish lysozyme than on those leading to mammal and bird lysozymes.

Amino Acid Sequence↗
PubMed1982

Presence of albumin mRNA precursors in nuclei of analbuminemic rat liver lacking cytoplasmic albumin mRNA.

Analbuminemic rats, which lack serum albumin, were previously found to have no albumin mRNA in the cytoplasm of the liver. In the present study, the existence of nuclear albumin mRNA precursors in the liver of analbuminemic rats was examined by RNA X cDNA hybridization kinetics. Albumin mRNA precursors were present in the nuclei of analbuminemic rat liver at almost normal levels, despite the absence of albumin mRNA from the cytoplasm. Nuclear RNA of analbuminemic rat liver was subjected to electrophoresis on 1% agarose gel in parallel with nuclear RNA of normal rat liver. RNA was transferred from the gel to diazobenzyloxymethyl-paper and hybridized to cloned cDNA. Several bands of putative albumin mRNA precursors were obtained with nuclear RNA of analbuminemic rat liver and some of them were indistinguishable from those of normal rat liver. Nuclear RNA of analbuminemic rats was hybridized to 3'-end-labeled cloned cDNA under the conditions of RNA excess and then digested completely with S1 nuclease and subjected to electrophoresis on polyacrylamide gel. By this technique, nuclear RNA that could hybridized to cDNA was found to have the albumin mRNA sequence in at least the 3' half of the mRNa that was covered by cloned cDNA. For comparison of the structures of the albumin genes of analbuminemic and normal rats, DNAs from rat livers of both types were digested completely with EcoRI, HindIII, and Pst I; the fragments were separated by electrophoresis on 1% agarose gel, transferred to nitrocellulose paper, and hybridized to cloned cDNA. The intensities of the corresponding bands and the digestion patterns of the analbuminemic and normal rat genes were indistinguishable. From these data, it is concluded that analbuminemic rats have a unique type of mutation(s) affecting albumin mRNA maturation.

Animals↗
PubMed2002

Upstream AUGs modulate prion protein translation in vitro.

The level of expression of the host PrP gene (PRNP) has been shown to affect the progression to a disease, transmissible spongiform encephalopathy (TSE). In order to define sequences that are responsible for translation ofPRNPmRNA we have investigated a region comprising its 5'-leader sequence. Most remarkable, it consists of an almost identical Kozak mRNA sequence and two AUG initiation codons which seem to modulate translation of the prion protein mRNA in vitro. Although transcriptional regulation of the prion protein PRNP gene had been expected to dominate the translational modulation, our observations point to a translational regulation of the mouse prion protein synthesis controlled by ribosomal entry and usage of AUG codons.

5' Untranslated Regions↗
PubMed1977

5' Terminal noncoding sequence heterogeneity in reovirus mRNA.

The nucleotide sequences of the mRNAs of reovirus appear to diverge near the 5' termini. Ribonuclease T1 digestion of methylated mRNA synthesized in vitro yielded seven different 5' terminal fragments of the form m7G5'pp5' GmpCpUp(Np)nGp. Chain length analysis showed that the parameter "n" in this structural formula assumes the values 3, 4 and 5.

Base Sequence↗
PubMed1979

Androgenic regulation of messenger RNA sequence complexity in accessory sexual tissues of the male rat studied with fractionated complementary DNA.

Effects of androgens on mRNA sequence complexity in the rat seminal vesicle have been investigated using complementary DNA fractionated on the basis of sequence abundance. Total cDNA complementary to poly(A)-rich RNA from normal rats was hybridised with an excess of the same RNA to controlled rot values and then the free cDNA was separated from cDNA . RNA hybrids by hydroxyapatite chromatography. Three cDNA fractions were obtained with very different hybridisation characteristics. Abundant cDNA hybridised to an excess of its parental RNA with an rot 1/2 of 2.46 x 10(-3) mol 1(-1) s and is complementary to about six or seven average-sized sequences. Use of hybrid-arrested translation in a cell-free protein-synthesising system has shown that this class of mRNA includes mRNAs coding for major androgen-dependent secretory proteins. Moderate and scarce cDNA fractions each showed more complex hybridization kinetics; computer analysis suggested each is complementary to two groups of average-sized sequences. Each cDNA fraction was hybridised to excess poly(A)-rich RNA from normal or castrated rats and the kinetics compared. Castration had no effect on the total number of sequences present in any class and did not alter the relative concentration of the scarce sequences. A small (threefold) decrease was seen in the concentration of abundant sequences with a larger (tenfold) decrease in the moderate class. Both de-reases were reversed by testosterone in vivo. The results are consistent with earlier studies where the effects of testosterone on seminal vesicle mRNA were followed using a translation assay and confirm that no gross differential effects are exerted on abundant mRNA coding for major secretory proteins. The cDNA fractions were also used to investigate the overlap in genetic expression between seminal vesicle and ventral prostate. Both tissues share all the scarce sequences in the same relative abundance. Less than 0.0015% and 0.004% of prostatic mRNA is complementary to seminal vesicle abundant and moderate sequences respectively. Similarly prostatic abundant sequences account for less than 0.004% of seminal vesicle mRNA.

Animals↗
PubMed1978

Recombinant DNA clones constructed from immunoglobulin kappa light chain messenger RNA.

Recombinant DNA clones have been generated from mouse myeloma MOPC 21 immunoglobulin kappa light chain mRNA. Complementary DNA (cDNA) synthesized on kappa light chain mRNA by reverse transcriptase was made double stranded and inserted into the bacterial plasmid vector, pMB9. Approximately 70 tetracycline-resistant transformed colonies containing kappa light chain mRNA sequences were identified by colony hybridization. Five of these recombinant clones were selected and characterized. Three clones contain both kappa light chain constant and variable region sequences. Two of these three recombinant clones have been shown to include all of the kappa light chain constant and variable region coding sequences. Another of the five selected recombinant clones contain kappa light chain constant region sequences. The remaining characterized clone appears to be derived from sequences at the 5'-end of kappa light chain mRNA, possibly extending to the terminal cap structure.

Base Sequence↗
PubMed1988

Selective expression of an erythroid-specific isoform of protein 4.1.

We have conducted comparative analysis of nucleotide sequences encoding erythroid and lymphoid protein 4.1 isoforms. The lymphoid protein 4.1 isoforms exhibit several nucleotide sequence motifs that appear to be either inserted into or deleted from the mRNA sequence by alternative splicing of a common mRNA precursor. One of these motifs, located within the spectrin-actin binding domain, is found only in erythroid cells and is specifically produced during erythroid cell maturation. The selective expression of the alternatively spliced mRNA during erythroid maturation implies the existence of a lineage-specific splicing mechanism whose activity is triggered by terminal maturation.

Amino Acid Sequence↗
PubMed1991

Cloning and characterization of the mouse cytochrome c oxidase subunit IV gene.

cDNA for mouse cytochrome c oxidase subunit IV (COXIV) was isolated by screening mouse liver and kidney cDNA libraries with a bovine COXIV cDNA probe. The 679-nucleotide nearly full length cDNA codes for a 22-amino acid presequence and a 147-amino acid mature protein which show 77 to 95% positional identity with the predicted sequences of human, bovine, and rat subunits. Screening of mouse genomic lambda EMBL3 library using the mouse cDNA probe yielded two overlapping clones. Restriction mapping and sequencing of the clones show that the mouse COXIV mRNA sequences are contained in five exons ranging from 58 to 236 base pairs, and four introns in a 7-kilobase region of the mouse genome. Southern blot analysis of restriction-digested genomic DNA indicates the presence of a single gene for COXIV in the mouse genome. Primer extension analysis using a synthetic 22-mer oligonucleotide, together with the 0.68-kilobase size of the mRNA shown by the Northern blot analysis, indicates that the major transcription start site of the COXIV gene is located 59 nucleotides upstream of the translation start site. The COXIV gene is highly GC rich and lacks TATA and CAAT elements in the immediate upstream region of the transcription start site. The putative promoter region, however, contains a number of GC boxes similar to those involved in the binding of Sp1 transcription factor. The unique features of the gene, as well as its characteristics common to other nuclear genes coding for different mitochondrial proteins, have been discussed.

Amino Acid Sequence↗
PubMed1992

Developmental and environmental concurrent expression of sunflower dry-seed-stored low-molecular-weight heat-shock protein and Lea mRNAs.

We have cloned and sequenced three different cDNAs from sunflower seed-stored mRNA. Sequence similarities and response to heat-shock identified one of the cDNAs as a low-molecular-weight heat-shock protein (lmw-HSP). The other two clones showed significant sequence similarity to the cotton and carrot late-embryogenesis-abundant (Lea) proteins D-113 and Emb-1, respectively. The three cDNAs showed similar expression patterns during zygotic embryo development, as well as in vegetative tissues of 3-day-old seedlings in response to stress. Maximal accumulation of all three mRNAs was detected in dry seeds and during embryo mid-maturation stage, in the absence of exogenous stress. In seedlings, mRNAs accumulated to lower levels in response to osmotic stress and exogenous abscisic acid (ABA) treatments. A differential time course of response to osmotic stress was observed: lmw-HSP mRNA accumulation was induced earlier than that of Lea mRNAs. The coordinate accumulation of Lea and lmw-HSP transcripts during embryo development and in response to stress and ABA suggests the existence of common regulatory elements for Lea and lmw-HSP genes, and supports the notion that HSPs might have alternative functions in the plant cell.

Abscisic Acid↗
PubMed1986

Human c-myb protooncogene: nucleotide sequence of cDNA and organization of the genomic locus.

We have isolated cDNA clones of the human c-myb mRNA that contain approximately 3.4 kilobases of the approximately 3.8-kilobase mRNA sequence. Nucleotide sequence analysis shows that the c-myb mRNA contains an open reading frame of 1920 nucleotides, which could encode a 72-kDa protein. The cDNA nucleotide sequence and the predicted amino acid sequence of the c-myb protein are highly homologous to the corresponding chicken and mouse proteins. In particular, a region toward the NH2 terminus of the protein containing a 3-fold tandem repeat of 51 residues is evolutionarily conserved and is the only region of homology with the Drosophila c-myb protein. This region may represent a functionally important structure, most likely the DNA-binding domain. cDNA clones have been used to isolate genomic clones and to define a preliminary intron/exon organization of the c-myb gene. Identification of 5' and 3' coding and noncoding exons indicates that the human c-myb locus spans a 40-kilobase region.

Amino Acid Sequence↗
PubMed1993

mRNA processing independent of RNase III and RNase E in the expression of the F1845 fimbrial adhesin of Escherichia coli.

F1845, the fimbrial adhesin of a diarrhea-associated Escherichia coli, confers upon the bacteria the ability to adhere to cultured epithelial cells in a diffuse pattern. The fimbrial subunit gene, daaE, is encoded on a polycistronic mRNA which is processed endoribonucleolytically to produce a stable message encoding only daaE. The processing event occurs in bacterial strains with mutations in RNase III or RNase E, the only endoribonucleases which have been implicated in the processing of E. coli mRNA. Sequences encoding a stem-loop structure downstream of daaE play an essential role in determining the stability of the daaE mRNA. Rapid degradation of the sequences upstream of the cleavage site occurs upon processing, suggesting that processing of the F1845 polycistronic mRNA results in differential expression of genes involved in the biogenesis of fimbriae.

Adhesins, Escherichia coli↗
PubMed1980

Heterogeneity of poly(I) x poly(C)-induced human fibroblast interferon mRNA species.

Three classes of human interferons (IFNs) have been defined on the basis of their immunological properties: the 'Le' or 'alpha' IFN, mainly derived from leukocyte or lymphoblastoid cells; the 'F' or 'beta' IFN, mainly derived from fibroblast cultures; and the 'T', 'immune' or 'gamma' IFN, mainly derived from mitogen- or antigen-stimulated lymphoid cells. Whereas several individual species of Le IFN have been purified to homogeneity, it is generally considered that F IFN represents a single protein. Thus current efforts to clone human fibroblast IFN mRNA sequences are based on the observation that F IFN mRNA sediments in sucrose gradients as a single RNA species of size corresponding to 12-14 S (refs 7-10). We show here, using gel electrohporesis of mRNA, that two populations of translationally active human fibroblast IFN mRNA molecules exist--an abundant '14 S' species and a scarce '11 S' species. Microinjection of either species of mRNA into Xenopus oocytes leads to the synthesis of biologically active F-type human IFN. These data agree with and complement recent RNA hybridization studies of Weissenbach et al.

Animals↗
PubMed2004

Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system.

The dependence of efficiency of translation initiation on mRNA sequence parameters was investigated in an Escherichia coli in vitro expression system. We designed a large-scale expression experiment focussing on the influence of sequence variations in the translated region (TR) of the mRNA without changing the 5'-untranslated region (5'-UTR). The level of translated protein from 756 expression constructs was measured and the influence of a large number of possible effector attributes was statistically analyzed. Base exchanges immediately adjacent to the start codon up to nucleotide (+)25 had a profound effect on translational efficiency. Correlation analysis revealed a significant dependence on base pair probability and G+C content on the expression level, indicating that mRNA secondary structure in this region hampers translation. Using our training data, we developed a methodology to predict and improve the translation efficiency of open reading frames (ORFs).

Bacterial Proteins↗
PubMed1986

Coding sequence of the precursor of the beta subunit of rat propionyl-CoA carboxylase.

A cDNA encoding the cytoplasmic precursor of the beta subunit of the mitochondrial enzyme propionyl-CoA carboxylase (EC 6.4.1.3) was cloned and sequenced. The DNA sequence of 2070 nucleotides is almost identical in size to the major hybridizing mRNA from rat liver (2000 +/- 50 nucleotides), suggesting that the cloned DNA represents nearly all of the mRNA sequence. A polypeptide expressed in vitro from an mRNA transcript of this cDNA is indistinguishable in size from the beta subunit precursor (58,500 Da). An open reading frame of 1623 nucleotides, flanked by stop codons, encodes a polypeptide of 541 amino acids; the predicted amino acid sequence was confirmed as that of the beta subunit of propionyl-CoA carboxylase by matching it to the amino acid sequences of five peptides derived from pure mature rat enzyme. Although the exact length of the cleavable, NH2-terminal leader peptide has not been determined because the NH2-terminal residue of the mature subunit is blocked, the leader is most likely 40-42 amino acids in length and is highly positively charged. Computer-aided analysis of secondary structure suggests that the leader peptide consists of two alpha-helical segments, with the two most NH2-terminal arginine residues occupying opposite sites of the first helix; this helix has no apparent hydrophobic moment.

Amino Acid Sequence↗
PubMed1995

Abundance and half-life of the distinct oat phytochrome A3 and A4 mRNAs.

Gene-preferential oligonucleotide probes were used to determined the relative abundance and half-lives of distinct oat phytochrome A (PHYA) mRNAs. Oat PHYA mRNAs are highly conserved in the 5'-untranslated region and the coding region, but the 3'-untranslated region has an overall lower sequence conservation and was the source of gene-preferential probes. PHYA3 mRNA was estimated to be ca. 61% of the oat PHYA mRNA pool present in poly(A)+ RNA from dark-grown seedlings. The half-lives for PHYA3 and PHYA4 mRNAs were both estimated to be ca. 30 min, and a similar short half-life was estimated for the average PHYA mRNA. Sequence comparisons of PHYA mRNAs from four grass species identified conserved sequences within the 5'- and 3'-untranslated regions that might be important for PHYA mRNA degradation.

Avena↗
PubMed2002

Expression and cellular localization of a modified type 1 ryanodine receptor and L-type channel proteins in non-muscle cells.

Functional and molecular biological evidence exists for the expression of ryanodine receptors in non-muscle cells. In the present study, RT-PCR and 5'-rapid amplification of cDNA 5'-end (5'-RACE analysis) provided evidence for the presence of a type 1 ryanodine receptor/Ca2+ channel (RyR1) in diverse cell types. In parotid gland-derived 3-9 (epithelial) cells, the 3'-end 1589 nucleotide sequence for a rat RyR shared 99% homology with rat brain RyR1. Expression of this RyR mRNA sequence in exocrine acinar cells, endocrine cells, and liver in addition to skeletal muscle and cardiac muscle, suggests wide tissue distribution of the RyR1. Positive identification of a 5'-end sequence was made for RyR1 mRNA in rat skeletal muscle and brain, but not in parotid cells, pancreatic islets, insulinoma cells, or liver. These data suggest that a modified RyR1 is present in exocrine and endocrine cells, and liver. Western blot analysis showed L-type Ca2+ channel-related proteins in parotid acinar cells, which were of comparable size to those identified in skeletal and cardiac muscle, and in brain. Immunocytochemistry carried out on intact parotid acini demonstrated that the dihydropyridine receptor was preferentially co-localized with the IP3 receptor in the apical membranes. From these data we conclude that certain non-muscle cells express a modified RyR1 and L-type Ca2+ channel proteins. These receptor/channels may play a role in Ca2+ signaling involving store-operated Ca2+ influx via receptor-mediated channels.

Animals↗
PubMed2005

Detection of germline mutations of hMLH1 and hMSH2 based on cDNA sequencing in China.

AIM: To detect the germline mutations of hMLH1 and hMSH2 based on mRNA sequencing to identify hereditary non-polyposis colorectal cancer (HNPCC) families. METHODS: Total RNA was extracted from peripheral blood of 14 members from 12 different families fulfilling Amsterdam criteria II. mRNA of hMLH1 and hMSH2 was reversed with special primers and heat-resistant reverse transcriptase. cDNA was amplified with expand long template PCR and cDNA sequencing analysis was followed. RESULT: Seven germline mutations were found in 6 families (6/12, 50%), in 4 hMLH1 and 3 hMSH2 mutations (4/12, 33.3%); (3/12, 25%). The mutation types involved 4 missense, 1 silent and 1 frame shift mutations as well as 1 mutation in the non-coding area. Four out of the seven mutations have not been reported previously. The 4 hMLH1 mutations were distributed in exons 8, 12, 16, and 19. The 3 hMSH2 mutations were distributed in exons 1 and 2. Six out of the 7 mutations were pathological, which were distributed in 5 HNPCC families. CONCLUSION: Germline mutations of hMLH1 and hMSH2 can be found based on cDNA sequencing so as to identify HNPCC family, which is highly sensitive and has the advantages of cost and time saving.

Adaptor Proteins, Signal Transducing↗
PubMed1991

Multiple polyadenylation signals and 3' untranslated sequences are conserved between chicken and human cellular myosin II transcripts.

We have isolated a chicken cellular myosin II heavy chain isoform cDNA clone that overlaps the published sequence for MHC-A (Shohet et al., 1989, Proc Natl Acad Sci 86, 7726-7730) and contains three canonical AAUAAA-polyadenylation signals in an additional 374 nucleotides at its 3' end. S1 nuclease protection analysis and PCR-amplification of MHC-A cDNA 3' ends have confirmed that all three of the signals are used in vivo. Differential usage of these signals without differential splicing in this region yields three messages that differ at their 3' ends but appear to encode the same protein. Comparison of the new chicken sequence with the homologous human MHC-A cDNA sequence (Saez et al., 1990, Proc Natl Acad Sci 87, 1164-1168) has revealed a number of similarities at this end of their long 3' untranslated regions (3'-UTRs). The three chicken polyadenylation signals reported here are positioned similarly to three signals evident in the human sequence. This region also contains distinct stretches of identity that are interspersed with regions of little homology. Within these regions of identity are a number of conserved sequence motifs, some of which have been demonstrated to be involved in mRNA metabolism in other systems. The pattern of mRNA sequence conservation demonstrated here suggests that the mechanisms for regulating MHC-A mRNA metabolism have been conserved between chickens and humans.

Animals↗