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At least 487 records · Page 27Linked to original sources
PubMed2001

The path of messenger RNA through the ribosome.

Using X-ray crystallography, we have directly observed the path of mRNA in the 70S ribosome in Fourier difference maps at 7 A resolution. About 30 nucleotides of the mRNA are wrapped in a groove that encircles the neck of the 30S subunit. The Shine-Dalgarno helix is bound in a large cleft between the head and the back of the platform. At the interface, only about eight nucleotides (-1 to +7), centered on the junction between the A and P codons, are exposed, and bond almost exclusively to 16S rRNA. The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting.

Bacteriophage T4↗
PubMed1980

The gene for polypeptide IX of adenovirus type 2 and its unspliced messenger RNA.

A 606 base pair segment of adenovirus type 2 DNA which includes the gene for polypeptide IX and its flanking regions has been sequenced. Comparison with the sequence of a cDNA copy of the 9S mRNA for polypeptide IX and direct analysis of its capped oligonucleotide show that the gene and its mRNA are colinear. The 9S mRNA has a length of 485 nucleotides, excluding the poly(A) tract and the m7G of the cap, and contains one single open translational reading frame which is sufficiently long to encode polypeptide IX. This reading frame contains three AUG codons, the first of which is used for initiation of protein synthesis. The mRNA has a 5' noncoding region of 24 nucleotides, excluding the m5G of the cap, and encodes a polypeptide which is 139 amino acids long and unusually rich in serine and alanine. The sequence TATATAA is found 25 nucleotides upstream from the cap site. The polyadenylation site has been identified but cannot be located unambiguously because of the presence of two A residues in the DNA sequence at this position. The 3' noncoding region is 41--43 nucleotides long and contains the hexanucleotide sequence AAUAAA. The mRNA for polypeptide IVa2 is encoded adjacent to that for polypeptide IX and is transcribed in the opposite direction. Sequence analysis revealed an overlap of 11--16 nucleotides, depending on the precise location of the polyadenylation sites, between 3' ends of these mRNAs.

Adenoviruses, Human↗
PubMed1998

NPY messenger RNA is increased in medial hypothalamus of anorectic tumor-bearing rats.

Previous investigations suggest that neuropeptide Y (NPY) feeding mechanisms and corticotropin releasing factor (CRF) are altered in anorectic tumor-bearing (TB) rats. To better determine the relationship of NPY and CRF synthesis to cancer anorexia we measured mRNA for these peptides in medial and lateral hypothalamus of TB and control rats. NPY and CRF mRNA were reliably detected by Northern blot analysis only in medial hypothalamus, where NPY message was elevated significantly in TB rats. CRF mRNA tended to be reduced in both pair-fed (PF) and TB rats, but did not reach statistical significance. Concentrations of NPY or CRF were not altered significantly in either the lateral or medial hypothalamus of TB or PF rats. These results suggest that the transcription of NPY is elevated in PF rats and is increased further in anorectic TB rats. The lack of significant increases in levels of peptides may be related to dilution, due to measuring a relatively large block of hypothalamic tissue. Alternatively, translation of the signal for NPY production may be inhibited, or degradation of peptide levels may be increased.

Animals↗
PubMed1995

Expression of epidermal growth factor receptor messenger RNA in human colorectal carcinomas assessed by non-radioactive in-situ hybridization.

No consensus as to the involvement of the epidermal growth factor receptor (EGF-R) in colorectal carcinomas has yet been attained, although they are assumed to play a role in the metastasis to lymph nodes and recurrence of breast carcinoma and bladder carcinoma invasion. Knowing that Dukes' classification of colorectal carcinoma is closely related to prognosis, we examined whether there is a correlation between Dukes' classification and the expression of EGF-R in colorectal carcinoma. If there is a positive correlation, the involvement of EGF-R in the processes may be assumed and the expression of EGF-R may be used as a marker of their prognosis. To this end, the expression of EGF-R mRNA and protein by non-radioactive in-situ hybridization and immunohistochemistry, respectively, were determined on histological preparations of formalin-fixed paraffin-embedded colorectal surgical specimens. In 30 cases of colorectal carcinoma examined, mRNA and/or protein was detected in 33% (two of six) of Dukes' A, in 40% (four of 10) of Dukes' B, in 36% (four of 11) of Dukes' C, in 33% (one of three) of Dukes' D and in 0% of normal colon epithelial cells. Thus, there was no positive correlation between the Dukes' classification and the expression of EGF-R. It is concluded that the expression of EGF-R in colorectal carcinoma is not a promising marker of prognosis. However, the role of EGF-R in EGF-R positive tumours remains to be examined.

Aged↗
PubMed1999

Messenger RNA in dormant cells of Sterkiella histriomuscorum (Oxytrichiade): indentification of putative regulatory gene transcripts.

In the absence of food, the oxytrichid Sterkiella histriomuscorum, like many ciliates, enters into dormancy and transforms into a round and walled encysted cell. When transferred back into a feeding medium, the cyst re-transforms into a vegetative cell in a few hours. This encystment-excystment pathway, which is common to many free-living and parasitic protists, is still poorly understood at the molecular level. In order to identify potential dormant transcripts in the cysts of Sterkiella, we have constructed cDNA libraries from mature cysts. Transcripts have been isolated confirming the presence of a mRNA pool in the dormant cells. The sequence analysis of two cDNA indicates open reading frames which show significant similarities to known proteins involved in mechanisms of regulation: 1) nifR3, an element of the nitrogen regulatory system in bacteria and 2) CROC-1, a newly identified human transcription factor. The two corresponding macronuclear genes represent the first putative regulatory genes isolated in ciliates. From a differential screening of the cDNA library against vegetative cDNA, one cyst-specific (and very abundant) transcript has been isolated but the product has not yet been identified. The possible involvment of these new ciliate genes in the excystment process is discussed.

Amino Acid Sequence↗
PubMedDate not supplied

A ribonuclease H-oligo DNA conjugate that specifically cleaves hepatitis B viral messenger RNA.

Ribonuclease H (RNaseH) recognizes and efficiently cleaves the RNA strand of DNA-RNA hybrids, but has no inherent sequence selectivity. However, the formation of DNA-RNA hybrids does require specific sequence recognition. On the basis of this concept, we wondered whether antisense oligonucleotides complementary to target RNA covalently linked to RNase H could be used to direct specific cleavage events mediated by RNase H. The aim of this research was to couple a DNA oligonucleotide to RNase H to confer specificity of ribonuclease activity toward hepatitis B viral (HBV) mRNA. A modified 13-base oligonucleotide that is specific for the DR1 region of HBV mRNA was conjugated to modified E. coli RNase H using a water soluble cross-linker. A 1200 base fragment of HBV RNA including the DR1 region was synthesized as a substrate using T7 RNA polymerase. Incubation of the RNase H-oligonucleotide conjugate with the RNA transcript resulted in cleavage of the HBV mRNA transcript in a concentration dependent manner. Eighty-five percent of substrate was cleaved under optimal conditions. Controls consisting of RNase H alone, oligonucleotide alone, and incubation of the conjugate with an unrelated mRNA substrate resulted in no cleavage activity. RNase H coupled to an HBV antisense oligonucleotide can specifically cleave target HBV transcripts.

Catalysis↗
PubMed1994

Arrangement of messenger RNA on Escherichia coli ribosomes with respect to 10 16S rRNA cross-linking sites.

The arrangement of the mRNA on the Escherichia coli ribosome with respect to ribosomal RNA sites has been investigated by photochemical cross-linking experiments. mRNA analogues 51-54 nucleotides in length contained a Shine-Dalgarno sequence, a single codon for tRNA(Gly), and 4-thiouridine (s4U) in the 5' third of the mRNA (-20 to -12), in the middle third of the mRNA (-3 to +6), or in the 3' third of the mRNA (+20 to +26), where the position numbers are counted from the first nucleotide of the codon. Complexes were formed with these mRNAs and 70S ribosomes in the absence or presence of tRNA(Gly) and were irradiated. The extent of cross-linking and the identity of cross-linked rRNA sites were determined on agarose gels and by primer extension. 16S rRNA nucleotides A412, A532, G693 (weakly), U723, and U1381 (weakly) cross-linked with s4U in the 3' third; A532, G693, U723, A1167 (weakly), U1381, G818 (weakly), and A845 cross-linked with s4U in the middle; A532, G693, U723, A1167, G818 (weakly), and A845 cross-linked with s4U in the 5' third. All of these cross-links occur with tRNA independence. Cross-links at C1395 and A1196 occur for all three mRNAs with tRNA dependence. The pattern of these sites provides information about the order of the rRNA sites along the mRNA track, and they also point out the apparent overlapping neighborhoods for the mRNA track. Models for the track of the mRNA on the 30S subunit are considered to explain this pattern of interactions.

Base Sequence↗
PubMed1991

Fluorescence study of the topology of messenger RNA bound to the 30S ribosomal subunit of Escherichia coli.

Short RNAs (25-36 nucleotides in length) with sequences of the translational initiation region of bacteriophage R17 protein A mRNA were produced by chemical and in vitro transcription techniques and labeled at their 5' or 3' ends with fluorescent probes. The interaction of these labeled RNAs with the 30S subunit of Escherichia coli was studied by using fluorescence spectroscopic techniques. All the RNAs bound tightly to 30S subunits (Kd less than or equal to 200 nM). Resonance energy transfer experiments demonstrated the proximity of the ends of the RNAs to each other and to two fluorescently labeled sites on the 30S subunit: the 3' end of 16S rRNA and the cysteine residue of ribosomal protein S21. By using the distances calculated from energy transfer between the 3' end of 16S rRNA and the ends of RNAs of varying lengths, a topological map of this region of mRNA on the 30S subunit was constructed.

Base Sequence↗
PubMed1985

Analysis of translational fidelity of ribosomes with protamine messenger RNA as a template.

A novel method was developed to estimate the translational fidelity of mammalian ribosomes in vitro with protamine mRNA of rainbow trout as template. Protamines are mixtures of basic proteins consisting of only seven types of amino acids (Arg, Ile, Val, Ser, Pro, Ala, and Gly), arginine (codon, AGR and CGN) being abundant. Taking advantage of the absence of lysine (codon, AAG) in the proteins, we determined the misincorporation of this amino acid into protamines in a cell-free translation system consisting of mouse liver ribosomes, protamine mRNA, [3H]lysine, [14C]arginine, and seven unlabeled amino acids: Ile, Val, Ser, Pro, Ala, Gly, and Met. After the reaction, translation products were analyzed by either sucrose gradient centrifugation or polyacrylamide gel electrophoresis. In the former method, radioactive protamines are mostly found on monosomes, but not on polysomes, probably because of the basic nature of the proteins. The error frequency was calculated from the molar ratio of [3H]lysine to [14C]arginine incorporated into protamines with an appropriate correction. The frequency was found to be 0.0006-0.002. This method enabled us to determine the frequency of misrecognition of purine bases at the second position of arginine codons in mRNA.

Amino Acid Sequence↗