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Chapter 39 : Translation Initiation in Bacteria

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Abstract:

This chapter summarizes the most important advances concerning structural and mechanistic aspects of translation initiation in bacteria which have occurred since the appearance of the last reviews on this subject. The small ribosomal subunit (30S) interacts with mRNA and fMet-tRNA in stochastic order to yield a bona fide 30S initiation complex through the rearrangement, kinetically controlled by the three initiation factors, of an unstable kinetic intermediate called the pre-ternary complex. Systematic variations of the translation initiation region (TIR) elements in the in vivo translation of reporter genes in and have produced similar results in two similar analyses. The differences observed in a study between heterologous and homologous proteins and the sometimes contradictory conclusions reached by similar studies concerning the relevance of specific TIR elements and the consequent criteria for optimization of translation remind us once again that each gene (mRNA) might be endowed with particular, not easily predictable properties. The dispensable nature of the Shine-Dalgarno (SD) sequence is evidenced by the existence of leaderless mRNAs which begin directly with an AUG initiation triplet. The recognition and binding of fMet-tRNA by IF2 play crucial roles in the translation initiation pathway of bacteria. The understanding of the translation initiation pathway cannot be considered satisfactory without full elucidation of the role played in this process by GTP and by the IF2-dependent GTPase.

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39

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Figures

Image of Figure 1
Figure 1

Scheme illustrating the cross-linking patterns of 4N/–3 mRNA (an mRNA with a 4-nucleotide spacer and a U residue at position –3) in its binary complex with the 30S ribosomal subunit in the presence of IF1, IF2, and IF3 and in the presence of IFs and fMet-tRNA. Compared to the simplest case of the 30S-mRNA complex (A), in which the mRNA is cross-linked almost exclusively to 1530 of 16S rRNA through its +2 position and to r-proteins S18 and S21 through its –3 position, the cross-linking pattern becomes much more complex in the presence of IFs (B): new, strong cross-links appear between S7 and both +2 and –3, and between S9 and +11, 1395 and +11, and 1360 and –3, while cross-linking of 1530 is partially shifted from +2 to –3. All these changes suggest a "leftward" shift of the mRNA with respect to the 30S subunit. A further rearrangement of the mRNA on the 30S subunit took place in the complete 30S initiation complex (C). Position +11 of the mRNA was no longer cross-linked to S9 and only marginally to 1395 but moved further leftward to cross-link to position 532 of 16S rRNA. Also, position +2 moved away from S7 and 1530, since cross-linking to these two elements was reduced, while +2 and –3 approached S9, with which a weak yet significant cross-linking was established. It should be noted that, in the course of the mRNA shift, the central base of the initiation triplet moves away from 1530 towards 1395, i.e., towards the P site of the subunit. The approximate relative positions of the relevant ribosomal components in the head or body of the 30S ribosomal subunit are shown. In the mRNA (solid bar), the initiation triplet and the positions of the potential cross-linking sites are indicated. Thick lines, major RNA-RNA cross-links; thin lines, major RNA-protein crosslinks; dotted lines, quantitatively minor cross-links of either type. The enclosure of 665 within a dotted box indicates the minor nature of this cross-link. (Taken from )

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 2
Figure 2

(A) Secondary structure of E. coli IF1 (taken from ). (B) Comparison of the 3-D structures of E. coli IF1 (gray) and cold shock protein CspA (white).

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 3
Figure 3

IF1 residues involved in 30S binding. Drawing of IF1 indicating the residues whose signals are broadened (dark gray) or shifted (black) upon binding to the 30S subunit. Residues whose mutagenesis affects ribosome binding are shown in light gray. (From )

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 4
Figure 4

Summary of the results obtained following site-directed mutagenesis of B. stearothermophilus IF2. The residual activity in fMet-tRNA binding displayed by each mutant is shown according to the indicated code.

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 5
Figure 5

fMet-tRNA binding site of IF2. The locations of the amino acid residues essential (red) and nonessential (yellow) for the interaction of IF2 with fMet-tRNA identified by site-directed mutagenesis are shown within the 3-D structure of IF2 C-2 (blue) determined by multidimensional heteronuclear NMR spectroscopy ( ).

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Figure 6

Differential intensity change of the backbone amide resonances of E. coli IF3 upon addition of 30S ribosomal subunits. The position of each amino acid in the primary sequence of IF3 is indicated in the abscissa; the ordinate presents the relative intensity change, (V – V0)/V0, of each assigned cross peak caused by the addition of E. coli 30S ribosomal subunits at a stoichiometric ratio, 30S/ IF3, of 0.2%. (From )

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 7
Figure 7

Active sites of E. coli IF3. The amino acid residues of the C domain (A and B) and N domain (C and D) of IF3 implicated in the interaction with the 30S ribosomal subunit as identified by NMR (A and C) and by site-directed mutagenesis and chemical modifications (B and D) are indicated with different colors (from blue to red according to relative NMR intensity changes, where red indicates the strongest effects) in the ribbon diagrams of the two domains. The coordinates of the structures were obtained from the Protein Data Bank (PDB). For the C domain, the NMR structure of the E. coli protein was used (PDB entry, 1IFE [ ]), and for the N domain, the X-ray structure of B. stearothermophilus protein was used (PDB entry, 1TIG [ ]). (From )

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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Image of Figure 8
Figure 8

IF3 docking on the 30S ribosomal subunit. The portions of the 16S rRNA helices are shown in black, but those which have been cross-linked to IF3 are shown in white. These are helix 45 in the upper part and helices 25 and 26 in the lower part of the diagram. The other nucleotides indicated are those protected by IF3 from kethoxal (yellow) and CMCT {N-cyclo-hexyl-N′-[2-(N-methylmorpholinio)ethyl]carbodiimide-p-toluene-sulfonate} (orange); G791 (pink) is partially protected from kethoxal and is functionally implicated by mutagenesis in IF3 binding. Also indicated are the nucleotides hyperreactive to dimethyl sulfate (green) and kethoxal (turquoise) and hypersensitive to RNase V1 (red) in the presence of IF3. The figure is taken from Sette et al., 1999, where additional information can be found.

Citation: Gualerzi C, Brandi L, Caserta E, La Teana A, Spurio R, Tomšic J, Pon C. 2000. Translation Initiation in Bacteria, p 475-494. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch39
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