Electron microscopic determination of the binding sites of ribosomal proteins S4 and S8 on 16S RNA.

Cole, Michael; Beer, M; Koller, Th.; Strycharz, William A.; Nomura, Masayasu

doi:10.1073/pnas.75.1.270

Cited by 24 publications

(9 citation statements)

References 19 publications

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“…Analogously, the regA protein could recognize a site of six nucleotides or so. A site of this size is compatible with the D (53)(54)(55)(56). However, given the genetics (Fig.…”

supporting

confidence: 54%

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

Karam¹,

Gold²,

Singer³

et al. 1981

Proc. Natl. Acad. Sci. U.S.A.

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The bacteriophage T4 gene regA encodes a protein that diminishes the expression of many unlinked early T4 genes. Previous work demonstrated that regA-mediated repression occurs after transcription. We report here on the identification of the target site on one regA-sensitive mRNA, the message encoding the phage T4 rUB protein. The target for regA-mediated action overlaps the translational initiation domain of the rIB messenger. The regA protein may be a repressor that operates translationally on a significant and interesting set of early phage T4 mRNAs.Evidence has accumulated over the last several years for control ofprokaryotic gene expression beyond the level oftranscription. Several factors may influence the translational yield from specific transcripts: discrimination by ribosomes in selecting one transcript over others, regulation of translation of particular mRNAs by repressors or activators, and destruction of transcripts at nonuniform rates. Direct evidence exists (in different systems) for all but one of these control mechanisms (1). The intrinsic strength of a ribosome binding site (refs. 1-7) determines the constitutivet level of specific translation, whereas regulation might encompass a reversible and specific repression or activation of translation through the intervention of a regulatory molecule. Alteration of transcripts by an RNase may be specific and, therefore, an example of irreversible regulation (8, 9). Reports of regulation of translation are rare: (i) the Escherichia coli RNA phages utilize translational regulation (10-14), (ii) the bacteriophage T4 controls the expression of its major DNA binding protein through autogenous translational regulation (15-18), and (iii) translational regulation is responsible for the careful titration of the quantities of several ribosomal proteins in E. coli (19)(20)(21)(22). Compared with the abundant descriptions oftranscriptional regulation, the literature on prokaryotic translational control is not vast.Recently, a phage T4 function was discovered that plays a role in control of the translation of a number of phage transcripts. Mutations in the regA gene of T4 lead to overproduction of a small number of the proteins that are synthesized during the early stages of phage development (23)(24)(25)(26)(27). The effects of these mutations seem to be mediated by loss ofa diffusible substance, probably a protein (26). Some observations suggest that the regA protein functions at a posttranscriptional level. T4 regA mutations do not affect RNA synthesis, although the protein overproduction ofT4 regA-phage infections is accompanied by a prolonged functional lifetime for the corresponding mRNA (and by decreased breakdown of some phage RNA) (23,24,27,28 The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact. 4670Biochemistry: Karam et al.Measurement of Phage T4 rUB Protein Synthesis. The methods for label...

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“…Analogously, the regA protein could recognize a site of six nucleotides or so. A site of this size is compatible with the D (53)(54)(55)(56). However, given the genetics (Fig.…”

supporting

confidence: 54%

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

Karam¹,

Gold²,

Singer³

et al. 1981

Proc. Natl. Acad. Sci. U.S.A.

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“…First, it is likely that protein S4 occupies some central position in the 30S particle: (i) it is distinguished by the most reported crosslinks and interactions with other proteins (4, 6, 10, 28); (ii) it has no antigenic determinants on the surface of the particle and thus is buried inside (30); (iii) it is bound simultaneously with several extended but noncontiguous regions of the 16S RNA chain (28,31,32). The central position and the unique binding of globular protein S4 to remote long sections of the RNA chain could be realized in the most natural way if it was positioned between the two branches of the Y-shaped RNA molecule, interacting with both the branches.…”

mentioning

confidence: 99%

Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

Spirin¹,

Serdyuk²,

Shpungin³

et al. 1979

Proc. Natl. Acad. Sci. U.S.A.

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In considering the structure of the 30S subunit of the Escherichia coli ribosome, we have assumed that: (l) all or almost all the proteins within the 30S particle are compact and globular, as recently shown for the isolated proteins S4, S7, S8, S15, and S16 in solution [Serdyuk, I. N., Zaccai, G. & Spirin, A. S. (1978) In recent years, the technique of chemical crosslinking of neighboring proteins by bifunctional reagents and measurements of the distances between deuterated or fluorescent-labeled proteins by using neutron scattering or energy transfer techniques, respectively, have contributed much to the knowledge of the protein topography in ribosomal particles and especially in the ribosomal 30S subunit of Escherichia coli. From these and a number of less direct data, several models of the topography of ribosomal proteins in the 30S particle have been proposed (1)(2)(3)(4)(5)(6)(7)(8). Independently, the use of the immunoelectron microscopy technique has also led to two different models of the topography of ribosomal proteins on the surface of the 30S particle (9-12; see also ref. 13).However, two complications have hampered further progress. First, no information was available as to three-dimensional structure and morphology of the 16S RNA; this RNA is known to be a structural backbone for arrangement of ribosomal proteins. Second, immunoelectron microscopy (9, 10) and neutron scattering (14, 15) data on proteins within the 30S subunit, as well as some physical measurements of isolated ribosomal proteins (16-21), have suggested strongly elongated or very expanded shapes of many ribosomal proteins; this led to ambiguity in interpretation of the results on chemical crosslinking, energy transfer, etc.Most recently, a specific compact conformation of the 16S RNA has been visualized by electron microscopy (22). On the other hand, a number of ribosomal proteins, such as S4, S7, S8, S15, and S16, have been reinvestigated and found to be compact globular proteins with cooperative tertiary structures (23)(24)(25). Based on these new results and using the numerous data reported on mutual arrangement (topography) of ribosomal proteins, we have constructed a model of the quaternary structure of the ribosomal 30S particle and then checked it by neutron and x-ray scattering experiments.MODEL CONSTRUCTION Initial Assumptions. In constructing the model, we have adhered to the size and the asymmetric three-dimensional structure of the ribosomal 30S subunit first deduced by one of us from electron microscopy of freeze-dried and shadow-cast samples of the particles (26). Morphologically, the 30S particle was found to be subdivided into a "head," a "body," and a side "bulge" (Fig. 1). A similar subdivision of the 30S particles, with a side "platform," was reported also by Lake and Kahan (11) and Lake (27) on the basis of electron microscopy of negatively stained samples.We have proceeded from two principal assumptions: (i) RNA within the 30S particle has a specific V-like or Y-like conformation (Fig. 1), as it is visu...

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“…These regions with large variation are often characterized by a high incidence of imperfect base pairs (U-G and A-G) in the helices. It has been shown that many of these irregular helices bind ribosomal proteins; for example, ribosomal protein S8 binds to the region 588 to 652 (Cole et al, 1978;Olins and Nomura, 1981). It has been proposed that the binding of protein stabilizes the helix and thereby allows more nonpairing or formation of weak base pairs (Noller and Woese, 1981).…”

Section: Discussionmentioning

confidence: 99%

“…This region is the binding site for protein S8 in E. coli and in archaebacteria (Cole et al, 1978;Olins and Nomura, 1981). This region also accounts for the large increase in size of the 18S rRNA of eukaryotes (Zweib et al, 1981).…”

Section: Region 588 To 651mentioning

confidence: 97%

The Sequence of 16S rRNA FromMycoplasmaStrain PG50

Frydenberg¹,

Christiansen²

1985

DNA

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The DNA sequence of one of the 16S rRNA genes (cistron rrnA) of Mycoplasma strain PG50 was determined. It is 1523 bp long and has about 70% homology to the sequence of Escherichia coli 16S rRNA (rrnB). The G + C content of the sequence is 48% compared with 56% G + C in the E. coli sequence. The secondary structure is formed and it is determined that most of the differences between the two sequences are seen in stems while loops in the secondary structure are conserved. A detailed description of differences and similarities to known sequences and rRNA oligonucleotide catalogues is given, and this information is used to discuss functional properties and phylogenetic relations of mycoplasma 16S rRNA.

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Electron microscopic determination of the binding sites of ribosomal proteins S4 and S8 on 16S RNA.

Cited by 24 publications

References 19 publications

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

Quaternary structure of the ribosomal 30S subunit: model and its experimental testing.

The Sequence of 16S rRNA FromMycoplasmaStrain PG50

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