Initiator‐tRNA recognizes a tetranucleotide codon during the 30 S initiation complex formation

Manderschied, U.; Bertram, Sabine; Gassen, Hans Günter

doi:10.1016/0014-5793(78)80321-4

Cited by 25 publications

(15 citation statements)

References 24 publications

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“…It has been suggested that an extended anticodon of the fMet-tRNA f Met (i.e., bases 3Ј or 5Ј of the tRNA anticodon that base pair with bases 5Ј or 3Ј of the mRNA start codon) enhances the rate of formation and the stability of initiation complexes (60,63,80,123). The bases 5Ј of AUG markedly modulate initiation complex formation (60).…”

Section: Translational Initiationmentioning

confidence: 99%

Evolutionary Conservation of Reactions in Translation

Ganoza

Kiel

Aoki

2002

Microbiol Mol Biol Rev

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SUMMARY Current X-ray diffraction and cryoelectron microscopic data of ribosomes of eubacteria have shed considerable light on the molecular mechanisms of translation. Structural studies of the protein factors that activate ribosomes also point to many common features in the primary sequence and tertiary structure of these proteins. The reconstitution of the complex apparatus of translation has also revealed new information important to the mechanisms. Surprisingly, the latter approach has uncovered a number of proteins whose sequence and/or structure and function are conserved in all cells, indicating that the mechanisms are indeed conserved. The possible mechanisms of a new initiation factor and two elongation factors are discussed in this context.

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Section: Translational Initiationmentioning

confidence: 99%

Evolutionary Conservation of Reactions in Translation

Ganoza

Kiel

Aoki

2002

Microbiol Mol Biol Rev

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“…The sequence corresponding to the initiating codon for the /3 subunit is apparently d(A-T-G), which is preceded by the ribosome binding site d(G-A-G-G) (72-75). The d(A-T-G) triplet is followed by a purine nucleoside dG which, according to [41], increases the probability of initiation at just that site. Yet another argument in favor of this codon being the initiating one is the absence of the d(T-A-G) sequence for a stop codon in the preceding sequence for a distance of at least 50 nucleotides [42].…”

Section: Combining Determination Of the Dna Primary Structure With Stmentioning

confidence: 99%

The Primary Structure of Escherichia coli RNA Polymerase

Ovchinnikov¹,

Monastyrskaya²,

Gubanov³

et al. 1981

European Journal of Biochemistry

185

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The combined structural study of proteins and of their corresponding genes utilizing the methods of both protein and nucleotide chemistry greatly accelerates and considerably simplifies both the nucleotide and protein structure determination and, in particular, enhances the reliability of the analysis. This approach has been successfully applied in the primary structure determination of the fl and j' subunits of Escherichia coli DNAdependent RNA potynierase and of their structural genes, yielding a continuous nucleotide sequence (4714 base pairs) that embraces the entire rpoB gene, the initial part of the rpoC gene and the intercistronic region, together with the total amino acid sequence of the fl subunit, comprising 1342 residues, and the N-terminal sequence of the jl' subunit (1 76 residues).Elucidation of the transcription mechanism requires detailed knowledge of the active-center organization of RNA polymerase at the various stages of the RNA synthesis. This, in turn, can be obtained only after determining the primary and spatial structure of the enzyme.Earlier we had established the amino acid sequence of the x subunit of Escherichiu coli DNA-dependent RNA polymerase by resorting solely to the ordinary methods of protein chemistry [5]. In the case of the fl and p' subunits with their much higher molecular weights (= 155000 and z 165000, respectively) [6], such an approach could no longer suffice, in view of the difficulties in isolating and purifying the resulting fragments and in reconstituting the amino acid sequence via overlapping peptides [7].The progress in DNA sequencing methods and the possibility of using the genetic code to obtain information on the primary protein structure from the nucleotide sequences is an attractive way to circumvent such difficulties; although here, too, there are many pitfalls, requiring considerable caution to avoid possible sources of error.In the first place the mRNA can undergo processing, leading to erroneous deduction of the protein structure. Secondly, the protein itself can be processed. Thirdly, it is often difficult to recognize in the overall DNA structure the beginning of a structural gene. The criterion for this purpose is the presence of an initiating codon together with the adjacent sequences complementary to the 3' end of 16-S RNA [8,9]. Frequently more than one such combination can be found for one and the same protein. insertion) in the DNA sequence determination could lead to a completely erroneous amino acid sequence of the protein. Thus, primary structure determination of DNA cannot serve as a substitute for the direct sequencing of the protein.In view of this, we decided to utilize the methods of both protein and nucleotide chemistries, performing the parallel sequencing of the structural genes rpoB (jl subunit) and rpoC (jl' subunit) and of the corresponding proteins. Knowledge of the nucleotide sequence of the pertinent DNA segments would permit aligning of the peptide fragments from the protein analysis into an uninterrupted polypeptide chain. Such...

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“…Clearly, the abundance of suppressor activity in natural bacterial populations (17), as well as the use of a termination codon to encode selenocysteine (18), require that termination be context-dependent. Similar context effects have been shown to influence the fidelity of translation (19,20) as well as the efficiency of translation initiation (21)(22)(23).…”

mentioning

confidence: 97%

Nonrandom utilization of codon pairs in Escherichia coli.

Gutman

Hatfield

1989

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

251

226

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We have analyzed protein-coding sequences of Escherichia coli and find that codon-pair utilization is highly biased, reflecting overrepresentation or underrepresentation of many pairs compared with their random expectations. This effect is over and above that contributed by nonrandomness in the use of amino acid pairs, which itself is highly evident; it is much weaker when nonadjacent codon pairs are examined and virtually disappears when pairs separated by two or three intervening codons are evaluated. There appears to be a high degree of directionality in this bias: any codon that participates in many nonrandom pairs tends to make both over-and underrepresented pairs, but preferentially as a left-or righthand member. We show a relationship between codon-pair utilization patterns and levels of gene expression: genes encoding proteins expressed at high levels tend to contain more abundant, but more highly underrepresented, codon pairs, relative to genes expressed at low levels. The nonrandom utilization of codon pairs may be a consequence of their effects on translational efficiency, which in turn may be related to the compatibility of adjacent aminoacyl-tRNA isoacceptors at the A and P sites of a translating ribosome.

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Initiator‐tRNA recognizes a tetranucleotide codon during the 30 S initiation complex formation

Cited by 25 publications

References 24 publications

Evolutionary Conservation of Reactions in Translation

Evolutionary Conservation of Reactions in Translation

The Primary Structure of Escherichia coli RNA Polymerase

Nonrandom utilization of codon pairs in Escherichia coli.

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