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Biomedical subjects

P Stiegler

Publications and source records attributed to P Stiegler.

At least 55 records · Page 3Linked to original sources
PubMed1981

Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure.

Extensive studies in our laboratory using different ribonucleases resulted in valuable data on the topography of the E.coli 16S ribosomal RNA within the native 30S subunit, within partially unfolded 30S subunits, in the free state, and in association with individual ribosomal proteins. Such studies have precise details on the accessibility of certain residues and delineated highly accessible RNA regions. Furthermore, they provided evidence that the 16S rRNA is organized in its subunit into four distinct domains. A secondary structure model of the E.coli 16S rRNA has been derived from these topographical data. Additional information from comparative sequence analyses of the small ribosomal subunit RNAs from other species sequenced so far has been used.

Computers↗
PubMed1981

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.

This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.

Base Composition↗
PubMed1981

A general secondary-structure model for procaryotic and eucaryotic RNAs from the small ribosomal subunits.

A consensus on the folding of the Escherichia coli 16-S ribosomal RNA is emerging and several complete nucleotide sequences of small ribosomal subunit RNAs, covering diverse types of organisms and organelles, are now available. We therefore investigated the extent of both nucleotide sequence and secondary structure conservation that may exist between the E. coli 16-S RNA and other ribosomal RNAs. All the RNA molecules examined could be folded into secondary structure schemes that illustrated remarkable preservation of many structural motifs as well as striking nucleotide sequence conservation compared with the E. coli molecule. This study presents a unitary scheme for the structural organization of the small ribosomal subunit RNAs. The evolutionary constraints on both primary and secondary structures most likely reveal the basic role of some restricted RNA regions in the function of the ribosome.

Animals↗
PubMed1980

[Secondary and topographic structure of ribosomal RNA 16S of Escherichia coli].

We present a model for the secondary structure of 16S ribosomal RNA from E. coli. This model has been deduced by restricting the total number of theoretical base pairings using the following criteria: (1) susceptibility of residues towards enzymatic probes that are specific for either paired or single stranded regions; (2) reactivity of certain residues to chemical modification; (3) evidence for medium and long range interactions; (4) comparative analysis of ribosomal RNA sequences from other organisms.

Base Sequence↗
PubMed1980

The topography of the 5' end of 16-S RNA in the presence and absence of ribosomal proteins S4 and S20.

A ribonucleoprotein prepared by strong ribonuclease digestion of a complex of 16-S ribosomal RNA and proteins S4 and S20 from Escherichia coli has been characterized; its nucleotide sequence, the positions of enzyme cuts and the sequence excisions have been placed in the completed sequence of 16-S RNA. The positions and yields of enzyme cuts, and excisions of sequence, are compared with those of various ribonucleoproteins prepared with S4 or S20 alone, and with the ribonuclease-resistant S4 RNA prepared from renatured 16-s RNA in the absence of ribosomal protein. These data yield important information on the topography and organisation of the 5' third of the 16-s RNA which is selectively maintained in its native conformation by the bound proteins; they also provide criteria for testing secondary structural models of this region of 16-S RNA.

Base Sequence↗
PubMed1975

An investigation of the 16-S RNA binding sites of ribosomal proteins S4, S8, S15, and S20 FROM Escherichia coli.

The RNA binding sites of four 30-S ribosomal subunit proteins from Escherichia coli, namely S4, S8, S15, and S20 were prepared from reconstituted single protein - 16-S-RNA complexes by mild enzymic digestion of non-protected RNA regions. Oligonucleotide fingerprints of the protected RNA regions were obtained and their positions were located within the 16-S-RNA sequence. They were not completely contiguous regions of RNA; oligonucleotides had been excised from each of them. The binding sites of S4 and S20, and those of S8 and S15 showed overlapping. The specificity of the RNA binding sites was confirmed by a reconstitution method.

Bacterial Proteins↗
PubMed1975

The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. III. Further studies.

In this paper, we describe in detail the recent progress in the nucleotide sequence analysis of the 16S ribosomal RNA from E. coli. The sequence which has been partially or completely determined so far encompasses 1520 nucleotides, i.e. about 95 percent of the molecule. Possible features of the secondary structure are suggested on the basis of the nucleotide sequence and data on sequence heterogeneities, repetitions and the location of modified nucleotides are presented.

Alkaline Phosphatase↗
PubMed1975

Evidence for tertiary structural RNA-RNA interactions within the protein S4 binding site at the 5'-end of 16S ribosomal RNA of Escherichia coli.+.

Evidence is presented for tertiary structural interaction(s) (interactions(s) between two regions of an RNA molecule that are widely separated in the RNA sequence) within the 5'-one third of the 16S ribosomal RNA of Escherichia coli that constitutes the binding site of protein S4. The two main interacting RNA regions were separated by about 120 nucleotides (sections Q to M) of the 16S RNA sequence. A second, smaller gap, of 13 nucleotides, occurred within section C". The two main interacting regions contain about 150 nucleotides (sections H" to Q) and 160 nucleotides (sections M to C"). They are folded back on one another and, especially in the presence of protein S4, are strongly protected against ribonuclease digestion. The intermediate region (sections Q to M), however, is relatively accessible to ribonucleases in the S4-RNP. By partial removal of subfragments from the RNA complex it was possible to localise the two main interacting sites within sections H" - H and sections I" - C". Three main criteria for the specificity of the RNA-RNA interactions were invoked and satisfied. The possibility of other tertiary structural RNA-RNA interactions occurring in other regions of the 16S RNA is discussed. Finally, all the structural information on the S4-RNP is summarised and a tentative model is proposed.

Base Sequence↗
PubMed1975

Primary sequence of the 16S ribosomal RNA of Escherichia coli.

Recent progress in the nucleotide sequence analysis of the 16S ribosomal RNA from E. coli is described. The sequence which has been partially or completely determined so far encompasses 1520 nucleotides, i.e. about 95% of the molecule. Possible features of the secondary structure are suggested on the basis of the nucleotide sequence and data on sequence heterogeneities, repetitions and the location of modified nucleotides are presented. In the accompanying paper, the use of the nucleotide sequence data in studies of the ribosomal protein binding sites is described.

Bacterial Proteins↗
PubMed1975

Location and characteristics of ribosomal protein binding sites in the 16S RNA of Escherichia coli.

Specific binding sites for five proteins of the Escherichia coli 30S ribosomal subunit have been located within the 16S RNA. The sites are structurally diverse and range in size from 40 to 500 nucleotides; their functional integrity appears to depend upon both the secondary structure and conformation of the RNA molecule. Evidence is presented which indicates that additional proteins interact with the RNA at later stages of subunit assembly.

Bacterial Proteins↗
PubMed1974

Abnormal maturation of precursor 16S RNA in a ribosomal assembly defective mutant of E. coli.

The precursor and mature 16S ribosomal RNAs from a novel thermosensitive ribosomal assembly defective mutant of E. coli, in which genetic evidence suggests that the ribosomal protein S4 is altered, have been isolated and characterised by finger-printing methods. The precursor 16S RNA, which is accumulated at 42 degrees , appears to be identical with that present in wild-type strains, and with that previously described by other workers. However, the mature 16S RNA, which is contained in apparently normal functional 30S ribosomal particles synthesised at the growth-permissive temperature of 30 degrees , is incompletely trimmed and has either one or two additional nucleotides at its 5'-terminus. This might be due either to an accumulation of two late intermediates in the maturation process, or to mis-trimming of the RNA. Both possibilities suggest that the change in the protein S4 is not only responsible for the thermosensitive character of ribosomal assembly in this mutant, but also causes an alteration in the trimming site, affecting its recognition by the enzyme involved in the maturation.

Base Sequence↗