Регуляция терминации трансляции фактором инициации eIF4F и сетью взаимодействующих с ним белков / Regulation of translation termination through network of interaction of eIF4F with other proteins тема диссертации и автореферата по ВАК РФ 00.00.00, кандидат наук Аль Шейх Валаа

• Аль Шейх Валаа
• кандидат наук
• 2026

Оглавление диссертации кандидат наук Аль Шейх Валаа

Table of Contents

LIST OF ABBREVIATIONS

INTRODUCTION:

Relevance of the research

Primary goals and objectives of the study

Scientific novelty:

Theoretical and practical significance

Methodology and research methods

Statements to be defended

Structure and scope of the dissertation

Approbation of the work

CHAPTER 1. LITERATURE REVIEW:

1.1 Translation in eukaryotes: phases and regulatory complexity

1.1.1 Eukaryotic translation initiation

1.1.2 The elongation phase of eukaryotic translation

1.1.3 Termination of translation and ribosome recycling

1.2 The eIF4F Complex

1.2.1 Components of the eIF4F complex and their isoforms

1.2.2 Role of eIF4F in translation

1.2.3 Physiological relevance of eIF4F

1.3 The eIF3 complex:

1.3.1 Structure and Composition of eIF3

1.3.2 Role in Translation Initiation

1.3.3 Functional Implications of eIF3 in Cellular Contexts

1.4 Programmed Cell Death 4 (PDCD4): Structure, Functions, and Biological Roles

1.4.1 Structure and Features of PDCD4

1.4.2 PDCD4 in Translational Regulation

1.4.3 PDCD4 in disease context

1.5 Regulation of eIF3/eIF4F through upstream Signaling Pathways

1.6 Integration of Translation Phases: Cross-talk between initiation and termination via protein networks

CHAPTER 2. MATERIALS AND METHODS:

2.1 Materials:

2.1.1 Bacterial Strains and Plasmids:

2.1.2 Used Media:

2.1.3 Buffers and Reagents:

2.2 Methods:

2.2.1 mRNA Preparation:

2.2.2 Ribosome and Protein Preparation:

2.2.3 48S initiation complex assembly

2.2.4 Assembly of the Pretermination Complex on MVHL mRNA (preTC (MVHL)):

2.2.5 Toe-print assay:

2.2.6 GTPase assay:

2.2.7 Assembly of Pretermination Complex on Nluc mRNA ((PreTC Nluc)):

2.2.8 Termi-Luc, Peptide Release Analysis:

2.2.9 Ribosome and Ribosomal Complex Binding Analysis:

2.2.10 Protein Electrophoresis in Denaturing SDS-PAGE:

2.2.111 Western Blot Hybridization:

2.2.12 Cell free translation

2.2.13 Statistical Data Analysis:

CHAPTER 3. RESULTS:

3.1 The activity of eIF4F in termination of translation

3.1.1 The whole eIF4F complex has an impact on translation termination

3.1.2 eIF4G and its truncated forms stimulate GTPase activity of eRF3

3.1.3 eIF4G2 acts in translation termination more efficiently than p100 fragment of eIF4G1

3.1.5 eIF4B stimulates translation termination:

3.1.6 eIF4F subunits increase each other's activity during translation termination

3.1.7 eIF4A promotes the landing of eRF1 on the ribosome, and eIF4G promotes the dissociation of eRF1-eRF3a from the ribosome

3.2 The role of eIF3 in termination of translation

3.2.1 eIF3 increases rate of peptide release, induced by release factors

3.2.2 eIF3 stimulates GTPase activity of eRF3

3.2.3 eIF3 binds to preTC

3.3 eIF3, PABP and eIF4F cooperatively act in translation termination

3.4 Regulation of translation via PDCD4

3.4.1 PDCD4 suppresses early stages of initiation of translation before eIF4F formation

3.4.2 PDCD4's activity is not affected by PABP in translation and initiation

3.4.3 PDCD4 does not suppress eIF4A activity during translation termination

3.4.4 PDCD4 competes with eIF4G in translation termination

3.4.5 PDCD4 does not affect eIF3 activity during translation termination

CHAPTER 4. DISCUSSION

4.1 eIF4F role in Translation Termination

4.2 eIF3's Multifaceted Role in Translation Termination

4.3 The Role of PDCD4 in Regulating Translation Initiation and Termination

CONCLUSION

CONCLUSIONS

REFERENCES

Введение диссертации (часть автореферата) на тему «Регуляция терминации трансляции фактором инициации eIF4F и сетью взаимодействующих с ним белков / Regulation of translation termination through network of interaction of eIF4F with other proteins»

Introduction:

Relevance of the research

Translation, also referred to as protein biosynthesis, is a complex process through which the genetic information from mRNA is being decoded in the ribosome and converted into polypeptides. It can be divided into four stages, proceeding in chronological order, each of which being facilitated by its own factors: initiation, elongation, termination, and ribosome recycling. Translation takes place from the 5' to the 3' end of the mRNA strand, beginning with the recognition of the start codon and ending when a stop codon within the main reading frame is reached. Translation is conserved in pro- and eukaryotes, however eukaryotes use much more translation factors than procaryotes. In addition, due to the uncoupling of translation and transcription in the cytoplasm and nucleus, eukaryotes protect their mRNAs with a cap structure on the 5' end and a poly(A) tail on the 3' end. Due to protein-protein interactions between factors associated with cap and poly(A) tail of mRNA, the eukaryotic mRNA can form a closed-loop structure. Interactions between translation factors bound to opposite ends of mRNA allow the cell to employ an additional level of translational regulation.

One of the key factors involved in closed-loop structure formation is eukaryotic initiation factor 4F (eIF4F). eIF4F is a hetero-trimeric protein that plays a crucial role in the translation initiation. It is composed of three subunits: eIF4G, eIF4E and eIF4A. This multi-protein factor essentially acts as a mediator by bringing the ribosomes onto the mRNA through a dual interaction with eIF4E, the cap-binding protein, and eIF4G, the scaffold protein. eIF4F has an extensive network of interactions with other proteins that provides regulation of translation at various levels. For instance, the interaction of eIF4F subunit, eIF4A with eIF4B significantly increases the velocity of translation initiation. Similarly, the interaction of another eIF4F subunit, eIF4G and the poly(A)-binding protein (PABP) promotes the formation of the mRNA closed-loop structure, enhancing translation efficiency.

eIF4G also interacts on the 40S ribosomal subunit with the other eukaryotic initiation factor eIF3. eIF3 in turn is a critical component of the translation machinery that binds to the 40S ribosomal subunit and promotes further interactions with other initiation factors and mRNA. eIF3 consists of 12 subunits in addition to the associated factor eIF3j and is an indispensable key player for ribosome binding that increases the efficiency of recruitment of other factors to the small subunit. The direct interaction of eIF3 with eIF4G promotes the binding of the 43S pre-initiation complex to the mRNA. The eIF3-eIF4F interaction is a pivotal step in translation initiation, enabling efficient protein synthesis. Additionally, eIF3 is involved in regulation of translation termination

modulating stop codon recognition and stimulating stop codon readthrough events in human and yeasts.

Another protein involved in eIF4F network is programmed cell death protein 4 (PDCD4). PDCD4 is a tumor suppressor, whose activity manifests by binding to eIF4A, thereby preventing its helicase activity, which is critical for the formation of the 48S complex and scanning the 5' untranslated region (5'UTR) of the mRNA. This protein contains similar domains to eIF4G and also increases translation termination efficiency.

The obtained data shows that eIF4F interaction with PABP may affect termination efficiency and thus likely connect the initiation and termination stages mechanistically and structurally. We also found that eIF4F promotes translation termination. In particular, eIF4A promotes release factor eRF1 loading into the ribosomal A site and eIF4G stimulates hydrolysis of GTP by eRF3. Interestingly, it was also found that eIF4G2 (also recognized as DAP5) may even work in translation termination like eIF4G. Using truncated forms of eIF4G - p100, p50, MA3, W2, and eIF4G2 - p86, we have pinpointed the MIF4G domain as the minimal region necessary for its role in termination of translation. Additionally, we have shown that eIF4B is able to stimulate translation termination both alone and in the presence of eIF4G and PABP. Moreover, we revealed that eIF3 promotes translation termination by enhancing the stop codon recognition and the release of the peptide. More specifically, eIF3 facilitates the loading of eRF1 into the A site of the ribosome, which stimulates the GTPase activity of eRF3 leading to an increased rate of peptide release.

Furthermore, in this research we also investigated the role of PDCD4 as a regulator involved in translation initiation and termination. The data obtained showed that in the presence of the purified eIF4F complex, PDCD4 did not hinder the assembly of the 48S preinitiation complex. Conversely, PDCD4 inhibited activation of the helicase of eIF4A during 5'UTR scanning by the 48S complex independent of any interaction with eIF4G. Notably, PDCD4 did not disturb eIF4A activity at the termination of translation, which indicates that its regulation of eIF4A is stage-specific, limited to initiation. Besides, PDCD4 competes with eIF4G for translation termination, which suggests that PDCD4 has a complex molecular mechanism targeting different players to control other stages of translation.

In summary, this study underscores the dual functions in translation of eIF4F and factors involved into its network - eIF3, eIF4B and PDCD4; it shows that these factors associated mostly with initiation can play important roles in termination as well. This brings about an understanding of the mechanism of translation at a molecular level and importance of multifunctionality of key

translation factors. By unraveling the relationship between initiation and termination factors, this work provides a framework for further exploration of translational regulation and its implications in cellular and disease contexts.

Primary goals and objectives of the study Goal of the study

The primary goal of this study is to investigate the role of eIF4F and proteins involved in its network, traditionally associated with translation initiation, in translation termination, and to elucidate the molecular mechanisms underlying their dual functionality in regulating different stages of translation.

Objectives of the study

1. Analyze the role of eIF4F and its individual subunits in translation termination,

2. Determine the activity of eIF4B in translation termination,

3. Characterize the role of eIF3 in translation termination,

4. Examine the Regulatory Role of PDCD4 in translation.

Scientific novelty:

The findings that are exhibited in this dissertation are novel and are being reported for the first time. First of all, this study complements the conventional view that eukaryotic initiation factors eIF3, eIF4F and eIF4B are involved exclusively in the initiation phase of translation, revealing that they are also important in translation termination. eIF3 facilitates termination through eRF1 loading into the ribosome, eIF4B stimulates binding of release factors to the ribosome and eIF4F has been shown to greatly enhance the efficiency of different stages of termination through its subunits. eIF4A supports the eRF1 loading and eIF4G stimulates eRF3 activity and dissociation of release factors. Additionally, this study for the first time describes the termination activity of second isoform of initiation factor eIF4G - eIF4G2 / DAP5. Also, the molecular mechanism of translational control by the tumor suppressor protein PDCD4 was clarified. It was shown that PDCD4 inhibits initiation not only by binding with eIF4A, but also via binding with the ribosome. And binding with PABP allows to realize a more complex control system across different translation stages.

These results point on the dual role of eIF3, eIF4B and eIF4F in translation, concerning the intricate coordination between translation initiation and termination. This research significantly contributes to the field of translational control, opening some of the new directions meant for studying its relevance to cellular function and disease.

Theoretical and practical significance

The present study demonstrates significant contribution toward broadening the horizons of understanding the fundamental basis of eukaryotic translation, more so, with regard to the dual roles that eIF3, eIF4B and eIF4F play in this process. These findings discover new ways on how de-coupled stages of translation can be coordinated, ultimately deepening our understanding of the molecular mechanisms that control protein biosynthesis. Such results would encourage subsequent research on the interaction between initiation and release factors or on their joint functionalities. This work may stimulate the development of the new research of translation. The results of this research could potentially be demand in development new therapies for diseases associated with abnormal translation termination on premature stop codons, for example, cancer and neurodegenerative disorders. Moreover, this research holds the potential to optimization of the biosynthesis of recombinant proteins in biotechnology, enabling the efficient production of therapeutic proteins and other bioengineered products.

Methodology and research methods

The application of advanced and classical molecular biology methods was employed in this work. During this investigation a reconstituted in vitro mammalian translation system was employed in understanding the mechanisms by which some additional factors contribute toward the termination of translation. To assemble pre-termination complexes (pre-TCs), purified components such as human and rabbit ribosome fractions, human initiation and elongation factors, mRNA, and tRNA were utilized. Functional studies were undertaken on purified pre-TCs, to assess the activities of release factors, with and without addition of the specific proteins of interest.

Translation termination has been examined using several techniques: toeprinting assay to detect different ribosomal complexes; peptide release assay to estimate efficiency of peptide-tRNA hydrolysis; and ribosome-factor interactions were evaluated by sucrose gradient centrifugation of ribosomal complexes followed by protein detection using Western blotting.

Statements to be defended

1. eIF4F is directly involved in the termination of eukaryotic translation due to the joint work of eIF4G and eIF4A.

2. The MIF4G domain has a vital role in activity of eIF4G in translation termination.

3. eIF4A binds to terminating ribosome in the presence of ATP and promotes eRF1 binding to the ribosome.

4. eIF4B simulates translation termination.

4. eIF3 promotes binding of eRF1 to the ribosome.

5. PDCD4 does not affect the assembly of the 48S preinitiation complex in the presence of the eIF4F complex.

6. PDCD4 competes with eIF4G in translation termination. Structure and scope of the dissertation

Dissertation consists of 4 chapters plus the introduction and conclusion. The complete volume of the dissertation consists of 111 pages, including 43 figure and 4 tables. Bibliography consists of 329 references.

Approbation of the work

The results obtained during the course of this dissertation were published in the form of 3 articles in peer-reviewed scientific journals and presented at 5 conferences.

Articles

□ Shuvalova E, Shuvalov A, Al Sheikh W, Klishin A, Biziaev N, Alkalaeva E. Eukaryotic initiation factor eIF3 facilitates loading of eukaryotic release factor eRF1 or suppressor tRNA to the ribosome. Nucleic Acids Res. 2026;54(1). doi:10.1093/NAR/GKAF1372

□ Shuvalova E, Al Sheikh W, Shuvalov A, Terenin IM, Alkalaeva E. Eukaryotic translation initiation factor 4F: functional properties and physiological role. Nucleic Acids Res. 2025;53(22). doi:10.1093/NAR/GKAF1351

□ Shuvalova E, Shuvalov A, Al Sheikh W, et al. Eukaryotic initiation factors eIF4F and eIF4B promote translation termination upon closed-loop formation. Nucleic Acids Res. 2025;53(5). doi:10.1093/NAR/GKAF161

CONFERENCES

• W. Al Sheikh, E. Shuvalova, A. Shuvalov, N. Bizyaev, E. Alkalaeva. «Eukaryotic initiation factor 4F enhances peptide release during the translation termination process.» 65-я Всероссийская научная конференция МФТИ, В честь 115-летия Л.Д. Ландау

• В. Аль Шейх, Е. Шувалова , Е. Алкалаева « роль фактора инициации трансляции 4F в процессе терминации трансляции эукариот» МОБИ-ХимФарма2023

• Al Sheikh W., Shuvalova E.Y., Alkalaeva E. «Interplay between PDCD4 and eIF4G in Translation Termination: Insights into Protein Synthesis Regulation» Lomonosov.2024

• Шуваловa E. Ю., Шувалов А. В., Аль Шейх В., Бизяев Н. С., Алкалаева Е. З. Влияние фактора инициации трансляции eIF3 на эффективность терминации трансляции у

эукариот // Международный Конгресс «VIII Съезд Вавиловского общества генетиков и селекционеров, посвященный 300-летию российской науки и высшей школы», 1419 июня 2024 года .- Саратов

• Алкалаева Е.З., Шувалова Е.Ю., Шувалов А.В., Бизяев Н.С., Аль Шейх В. Регуляция терминации трансляции эукариот факторами инициаторного комплекса. // Биоинформатика регуляции и структуры геномов / системная биология: Четырнадцатая международная мультиконференция. Россия, Новосибирск, 5-10 авг. 2024 г.

Заключение диссертации по теме «Другие cпециальности», Аль Шейх Валаа

Conclusion

The termination phase of eukaryotic translation, though critical, has been less thoroughly investigated compared to initiation and elongation. This imbalance leaves significant gaps in understanding how translation is regulated as a whole. Efficient translation depends on the seamless interplay between the various phases (initiation, elongation, and termination) to ensure that the protein biosynthesis system operates with precision and adaptability.

The current research highlights the significant roles of translation initiation factors eIF4F, eIF4B and eIF3 in the termination phase. eIF4F, a cap-binding complex crucial for initiating translation, contributes to termination efficiency by stabilizing interactions between the ribosome, the mRNA and release factors at the stop codon. Similarly, eIF3, a multiprotein complex integral to ribosome recruitment during initiation, facilitates termination by coordinating the activity of release factors and promoting accurate stop codon recognition. These findings underscore the interconnectedness of translation phases, with initiation factors playing unexpected yet critical roles in termination.

Additionally, it also reveals that PDCD4, a known inhibitor of cap-dependent initiation, competes specifically with eIF4A, a subunit of the eIF4F complex, rather than with the entire eIF4F assembly. This targeted competition highlights a precise regulatory mechanism, allowing PDCD4 to influence translation termination dynamics without broadly disrupting eIF4F's overall function. These findings provide new insights into the complex regulatory interplay between translation factors, advancing the understanding of how the phases of translation are interconnected and finely tuned to ensure both efficiency and fidelity in protein synthesis.

Conclusions

• eIF4F is directly involved in the termination of eukaryotic translation due to the joint work of eIF4G and eIF4A

• The MIF4G domain of eIF4G has a vital role in stimulating GTPase activity of eRF3

• eIF4A binds to preTC with the presence of ATP-non hydrolyzed analogue (AMPNP) and promotes eRF1 binding to the ribosome

• eIF4B stimulates termination of translation.

• eIF3 facilitates the binding of eRF1 to the stop codon and stimulates peptide release

• eIF4F and eIF3 jointly participate in translation termination in the closed-loop structure

• PDCD4 does not affect the assembly of the 48S preinitiation complex in the presence of the eIF4F complex.

• PDCD4 competes with eIF4G and does not affect the activity of eIF4A in translation termination

Список литературы диссертационного исследования кандидат наук Аль Шейх Валаа, 2026 год

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