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The Cryo-Electron Microscopy Structure of a complete 30S Translation Initiation Complex from Escherichia coli Essay (Critical Writing)

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Summary

In their paper Julian et al (2011) notes that creation of composite structures of 30S is a necessary step in monitoring of gene forms. In the article “The Cryo-Electron Microscopy Structure of a complete 30S Translation Initiation Complex from Escherichia coli” Julian and others utilized Escherichia coli to illustrate the choice, precise start up codon, and structure of an absolute 30S Translation-Initiation process (Julian et al. 2011).

Since initiation is the phase whereby ribosome chooses mRNAs as per their translation-initiation sections (TIS) and finds an accurate visualizing structure, this stage need a lot of care otherwise the resulting structure would not be complete. The authors aimed at developing a novel Cryo-electron microscopy reformation of the entire 30S, comprising of mRNA and t-RNA structures.

They also aimed at showing that both the N-terminal region and C-terminal region of Escherichia coli are attached to the structure supported by the 30S micro unit.

Fastening of initiation elements together with mRNA triggers a shift of the main end in relation to the original structure of the 30S micro unit, which is probable to overcome via 50S micro unit supporting the hydrolysis/dissociation processes. The shape offers information regarding the action of mRNA choice during initiation phase. Synthesis of 30S translation structure heralds linkage to the 50S micro unit which then translates into the active ribosome (Allen et al. 2005).

Through a Cryo-EM concept to envision the various models without staining and/or fixation, the authors established the shape portrayed by an absolute 30S translation unit and evidently established the locations and arrangements of the t-RNA and the other three initiation elements.

The authors found that the absence of the translation elements and presence of the t-RNA trigger a shift of the end in relation to the entire structure supported by the 30S micro unit which are necessary for quick linking of the 50S micro unit and for purposes of monitoring choice of the m-RNA.

Also t-RNA did not feature in the 30S formation and thus the findings gave information regarding an impending function of deterring unification of the two ribosome based micro units. Such findings help to understand how the interaction between factors at the initial phases of transformation chooses the m-RNA and controls development of basic ribosome (Julian et al., 2011).

Critical Analysis

Recently, models regarding 30S IC structures without the IF3 (Brandi et al., 2007; Carter et al., 2001) and regarding the 70S IC having weight associated to IF3 (Dallas and Noller, 2001; Frank and Agrawal, 2000) have been identified. But the shape formed by the absolute 30S IC structure has been indescribable, perhaps because of intrinsic modelling forces directed to the 30S micro units.

Evaluation of the 50S model in terms of GTP-linked conditions of IF2 indicated that during pre-hydrolysis phase the 30S micro unit is positioned in a convoluted structure in relation to the 70S micro unit.

Based on this concept, one molecule details have indicated that binding all 50S micro unit to a single 30S structure at first develops into 70S structure with a convoluted orientation, and that GTP based hydrolysis caused by IF2 enhances the formation of non-convoluted structure, therefore allowing the ribosomal orientation to advance and reach the elongation state (Korostelev et al., 2007; Low and Lowe, 2006; McCarthy and Brimacombe, 1994).

Julian et al. (2011) illustrate the Cryo-electron microscopy reformation of a full 30S structure consisting of Ifs, t-RNA, and mRNA and determine the site and arrangement of both IF2 and IF3. Contrary to 30S structure derived without IF3 (Studer and Joseph, 2006), the full 30S structure presented by Julian and others shows an initiation linkage that is entirely capable in the choice of the precise start subunit.

The information indicate an alternation of the basic structure represented by 30S micro unit during the modelling of 30S micro unit and propose how the baseline shifts of the original 30S micro unit could impact 50S micro unit forming and mRNA choice.

Reformation of an absolute 30S structure

Julian and others synthesised 30S subunit based on E. coli 30S micro units, mRNA, and IFs analogy. The mRNA utilized in the composite construction was m002 that consists of both 5nt linkage and a 9nt SD connecting the start codon to the SD (Wintermeyer and Gualerzi, 1983).

Julian et al. (2011) argued that the elongated SD presents firm interfaces and considerably lowers the hydrolysis speed of IF3 (Korostelev et al., 2007); m002 resemble the mRNAs with an elongated SD utilized in past construction and bio-chemical researches (Brandi et al., 2007; Low and Lowe, 2006; Studer and Joseph, 2006).

Although the first pair of approximately 48, 500 atoms formed a Cryo-electron microscopy structure, the weight could not be evidently associated with IF3 and t-RNA embedded to the original 30S micro unit in regions anticipated from a past reformation study of the 30S micro units integrated with a composite translator IF2 and t-RNA.

But the weights presented by the authors in their first reformation failed to show structural information regarding the t-RNA, indicating heterogeneity of the specimen utilized because of the variations in the volume of the 30S micro units containing linkages and/or separate orientation phases.

Dissociation into 2 categories through non-controlled optimal probability-initiated categorization (Marshall, Aitken, & Puglisi, 2009), a newly adopted instrument that has been optimally utilized with many ribosomal specimens and self-induced image generating produced SD structures different from those portrayed in the article (Milon et al., 2008).

Segmentation

After take away the weight matching the 30S micro unit based on category 2 structure, regions occupied by t-RNA could be coded, which is in line with past reformation and biological researches (Marshall, Aitken, and Puglisi, 2009). The principal section of the final weight could be associated with the t-RNAfMet composite positioned along the breadth and also along the gap connecting the rear end and the main structure of the 30S micro unit.

The weight represented by IF1 was more consistent with past research, since its fastening region was occupied by the IF2 model. But marching the molecule representation of IF1 attached to the core structure of 30S micro unit (Dallas and Noller, 2001) showed that, in the structure presented in the article, IF1 can be attached to the region linking the IF2 and 30S micro unit in the gap left by the helix 44 and ribosome (Korostelev et al., 2007; Lomakin et al., 2006; Moreno et al., 1999).

Conclusion

The article aimed at developing novel Cryo-electron microscopy reformation of the entire 30S, comprising of mRNA and t-RNA structures. It also aimed at showing that both the N-terminal region and C-terminal region of Escherichia coli are attached to the structure supported by the 30S micro unit.

Evaluation of the 50S model in terms of GTP-linked conditions of IF2 is an indication that during pre-hydrolysis phase the 30S micro unit is positioned in a convoluted structure in relation to the 70S micro unit.

Based on this concept, it should be recommended that one molecule data is enough to indicate that binding all 50S micro unit to a single 30S structure at first develops into 70S structure with a convoluted orientation, and that GTP based hydrolysis caused by IF2 enhances the formation of non-convoluted structure, therefore allowing the ribosomal orientation to advance and reach the elongation state.

References

Allen G. S, Zavialov A, Gursky R, Ehrenberg M, Frank J 2005, ‘The Cryo-EM structure of a translation initiation complex from Escherichia coli,’ Cell, vol. 121, pp. 703–712.

Brandi L, Fabbretti A, Milon P, Carotti M, Pon C 2007, ‘Methods for identifying compounds that specifically target translation,’ Methods Enzymol, vol. 431, pp. 229–267.

Carter A. P, Clemons W. M Jr, Brodersen D. E, Morgan-Warren R. J, Hartsch T 2001, ‘Crystal structure of an initiation factor bound to the 30S ribosomal subunit,’ Science, vol. 291, pp. 498–501.

Dallas A, Noller H 2001, ‘Interaction of Translation Initiation factor 3 with the 30S Ribosomal subunit,’ Mol Cell, vol. 8, pp. 855–864.

Frank J, Agrawal K 2000, ‘A ratchet-like inter-subunit reorganization of the ribosome during translocation,’ Nature, vol. 406, pp. 318–322.

Julian P, Milon P, Agirrezabala X, Lasso G, Gil D, Rodnina M, Valle M 2011, ‘The Cryo-EM Structure of a Complete 30S Translation Initiation Complex from Escherichia coli,’ PLoS Biology, vol. 9, p. 7.

Korostelev A, Trakhanov S, Asahara H, Laurberg M, Lancaster L 2007, ‘Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome,’ Proc Natl Acad. Science U S, vol. 104, pp. 16840–16843.

Lomakin B, Shirokikh E, Yusupov M, Hellen U, Pestova V 2006, ‘The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH,’ Embo Journal, vol. 25, pp. 196–210.

Low H, Lowe J 2006, ‘A bacterial dynamin-like protein,’ Nature, vol. 444, pp. 766–769.

Marshall A, Aitken E, Puglisi D 2009, GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell 35: 37–47.

McCarthy E, Brimacombe R 1994, ‘Prokaryotic translation: the interactive pathway leading to initiation,’ Trends Genet, vol. 10, pp. 402–407.

Milon P, Konevega L, Gualerzi O, Rodnina V 2008, ‘Kinetic check point at a late step in translation initiation,’ Mol Cell, vol. 30, pp. 712–720.

Moreno M, Drskjotersen L, Kristensen E, Mortensen K, Sperling-Petersen U 1999,’ Characterization of the domains of E. coli initiation factor IF2 responsible for recognition of the ribosome,’ FEBS Lett, vol. 455, pp. 130–134.

Studer M, Joseph S 2006, ‘Unfolding of mRNA secondary structure by the bacterial translation initiation complex,’ Mol Cell, vol. 22, pp. 105–115.

Wintermeyer W, Gualerzi C 1983, ‘Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to the 30S ribosomal subunits,’ Biochemistry, vol. 22, pp. 690–694.

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IvyPanda. "The Cryo-Electron Microscopy Structure of a complete 30S Translation Initiation Complex from Escherichia coli." March 28, 2019. https://ivypanda.com/essays/the-cryo-electron-microscopy-structure-of-a-complete-30s-translation-initiation-complex-from-escherichia-coli/.

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IvyPanda. 2019. "The Cryo-Electron Microscopy Structure of a complete 30S Translation Initiation Complex from Escherichia coli." March 28, 2019. https://ivypanda.com/essays/the-cryo-electron-microscopy-structure-of-a-complete-30s-translation-initiation-complex-from-escherichia-coli/.

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IvyPanda. (2019) 'The Cryo-Electron Microscopy Structure of a complete 30S Translation Initiation Complex from Escherichia coli'. 28 March.

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