IRES-mediated cap-independent translation, a path leading to hidden proteome

Abstract Most eukaryotic mRNAs are translated in a cap-dependent fashion; however, under stress conditions, the cap-independent translation driven by internal ribosomal entry sites (IRESs) can serve as an alternative mechanism for protein production. Many IRESs have been discovered from viral or cellular mRNAs to promote ribosome assembly and initiate translation by recruiting different trans-acting factors. Although the mechanisms of translation initiation driven by viral IRESs are relatively well understood, the existence of cellular IRESs is still under debate due to the limitations of translation reporter systems used to assay IRES activities. A recent screen identified > 1000 putative IRESs from viral and human mRNAs, expanding the scope and mechanism for cap-independent translation. Additionally, a large number of circular RNAs lacking free ends were identified in eukaryotic cells, many of which are found to be translated through IRESs. These findings suggest that IRESs may play a previously unappreciated role in driving translation of the new type of mRNA, implying a hidden proteome produced from cap-independent translation.

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Circular RNA, the Key for Translation

International Journal of Molecular Sciences ◽

10.3390/ijms21228591 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8591

Author(s):

Anne-Catherine Prats ◽

Florian David ◽

Leila H. Diallo ◽

Emilie Roussel ◽

Florence Tatin ◽

...

Keyword(s):

Translation Initiation ◽

Translational Control ◽

Mrna Translation ◽

Circular Rna ◽

Initiation Factor ◽

Circular Rnas ◽

Strong Impact ◽

Initiation Rate ◽

New Family ◽

Independent Translation

It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m6A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5′ end-independent translation initiation. Today a new family of so-called “noncoding” circular RNAs (circRNAs) has emerged, revealing the pivotal role of 5′ end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3′–5′ interaction have been reported, including m6A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and noncovalently closed circular mRNA translation landscape shows that RNA with circular shape might be the rule for translation with an important impact on disease development and biotechnological applications.

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Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs

Comparative and Functional Genomics ◽

10.1155/2012/391546 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12 ◽

Cited By ~ 34

Author(s):

Encarnación Martínez-Salas ◽

David Piñeiro ◽

Noemí Fernández

Keyword(s):

Translation Initiation ◽

Internal Ribosome Entry Site ◽

Entry Site ◽

Internal Ribosome Entry ◽

Initiation Of Translation ◽

Multiple Processes ◽

Cellular Mrnas ◽

Eukaryotic Mrnas ◽

Internal Initiation ◽

Eukaryotic Organisms

The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. The majority of eukaryotic cellular mRNAs initiates translation by the cap-dependent or scanning mode of translation initiation, a mechanism that depends on the recognition of the m7G(5′)ppp(5′)N, known as the cap. However, mRNAs encoding proteins required for cell survival under stress bypass conditions inhibitory to cap-dependent translation; these mRNAs often harbor internal ribosome entry site (IRES) elements in their 5′UTRs that mediate internal initiation of translation. This mechanism is also exploited by mRNAs expressed from the genome of viruses infecting eukaryotic cells. In this paper we discuss recent advances in understanding alternative ways to initiate translation across eukaryotic organisms.

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Circular RNA, the Key for Translation

10.20944/preprints202010.0088.v1 ◽

2020 ◽

Author(s):

Anne-Catherine Prats ◽

Florian David ◽

Leila Diallo ◽

Emilie Roussel ◽

Florence Tatin ◽

...

Keyword(s):

Translation Initiation ◽

Translational Control ◽

Mrna Translation ◽

Circular Rna ◽

Initiation Factor ◽

Circular Rnas ◽

Strong Impact ◽

Initiation Rate ◽

New Family ◽

Independent Translation

It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m6A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5’end-independent translation initiation. Today a new family of non-coding RNAs, circular RNAs (circRNAs), has emerged, revealing the pivotal role of 5’end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3’-5’ interaction have been reported, including m6A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and non-covalently circular mRNA translation landscape shows that RNA circular shape is the rule for translation with an important impact on disease development.

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Unbiased screen of human transcriptome reveals an unexpected role of 3ʹUTRs in translation initiation

10.1101/2021.05.28.446092 ◽

2021 ◽

Author(s):

Zefeng Wang ◽

Yun Yang ◽

Xiaojuan Fan ◽

Yanwen Ye ◽

Chuyun Chen ◽

...

Keyword(s):

Cell Growth ◽

Translation Initiation ◽

Human Transcriptome ◽

Initiation Factors ◽

Regulatory Mode ◽

Translation Initiation Factors ◽

Eukaryotic Mrnas ◽

Independent Translation

Although most eukaryotic mRNAs require a 5ʹ-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we developed a circRNA-based system and unbiasedly identified more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3ʹUTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5ʹUTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5ʹUTR structures and facilitate ribosome scanning. Functionally, we showed that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5ʹUTR structure and a new 3ʹ-CiTI in response to hypoxia. Therefore, deletion of 3ʹ-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3ʹUTR actively participate in the translation initiation.

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A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate

eLife ◽

10.7554/elife.54575 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Ritam Neupane ◽

Vera P Pisareva ◽

Carlos F Rodriguez ◽

Andrey V Pisarev ◽

Israel S Fernández

Keyword(s):

Translation Initiation ◽

Functional Data ◽

Protein Production ◽

Domain Architecture ◽

Translation Regulation ◽

Viral Mrna ◽

Rna Sequences ◽

Internal Ribosomal Entry Sites ◽

Initiation Factors ◽

Initiation Stage

Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called Internal Ribosomal Entry Sites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs.

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Circular RNA, the Key for Translation

10.20944/preprints202010.0088.v2 ◽

2020 ◽

Author(s):

Anne-Catherine Prats ◽

Florian David ◽

Leila Diallo ◽

Emilie Roussel ◽

Florence Tatin ◽

...

Keyword(s):

Translation Initiation ◽

Translational Control ◽

Mrna Translation ◽

Circular Rna ◽

Initiation Factor ◽

Circular Rnas ◽

Strong Impact ◽

Initiation Rate ◽

New Family ◽

Independent Translation

It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m6A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5’end-independent translation initiation. Today a new family of so-called “non-coding” circular RNAs (circRNAs) has emerged, revealing the pivotal role of 5’end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3’-5’ interaction have been reported, including m6A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and non-covalently circular mRNA translation landscape shows that RNA circular shape might be the rule for translation with an important impact on disease development and biotechnological applications.

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ATP-Independent Initiation during Cap-Independent Translation of m6A-Modified mRNA

International Journal of Molecular Sciences ◽

10.3390/ijms22073662 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3662

Author(s):

Pavel A. Sakharov ◽

Egor A. Smolin ◽

Dmitry N. Lyabin ◽

Sultan C. Agalarov

Keyword(s):

Translation Initiation ◽

Mrna Translation ◽

Relative Resistance ◽

Lower Efficiency ◽

Free System ◽

Cell Free System ◽

Eukaryotic Mrnas ◽

A Cell ◽

First Time ◽

Independent Translation

The methylation of adenosine in the N6 position (m6A) is a widely used modification of eukaryotic mRNAs. Its importance for the regulation of mRNA translation was put forward recently, essentially due to the ability of methylated mRNA to be translated in conditions of inhibited cap-dependent translation initiation, e.g., under stress. However, the peculiarities of translation initiation on m6A-modified mRNAs are not fully known. In this study, we used toeprinting and translation in a cell-free system to confirm that m6A-modified mRNAs can be translated in conditions of suppressed cap-dependent translation. We show for the first time that m6A-modified mRNAs display not only decreased elongation, but also a lower efficiency of translation initiation. Additionally, we report relative resistance of m6A-mRNA translation initiation in the absence of ATP and inhibited eIF4A activity. Our novel findings indicate that the scanning of m6A-modified leader sequences is performed by a noncanonical mechanism.

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Relevance of Translation Initiation in Diffuse Glioma Biology and its Therapeutic Potential

Cells ◽

10.3390/cells8121542 ◽

2019 ◽

Vol 8 (12) ◽

pp. 1542 ◽

Cited By ~ 3

Author(s):

Digregorio Marina ◽

Lombard Arnaud ◽

Lumapat Paul Noel ◽

Scholtes Felix ◽

Rogister Bernard ◽

...

Keyword(s):

Translation Initiation ◽

Protein Production ◽

Therapeutic Potential ◽

Environmental Stressors ◽

Current Therapy ◽

Diffuse Glioma ◽

Overall Survival Rate ◽

Malignant Cells ◽

Translational Machinery ◽

Initiation Step

Cancer cells are continually exposed to environmental stressors forcing them to adapt their protein production to survive. The translational machinery can be recruited by malignant cells to synthesize proteins required to promote their survival, even in times of high physiological and pathological stress. This phenomenon has been described in several cancers including in gliomas. Abnormal regulation of translation has encouraged the development of new therapeutics targeting the protein synthesis pathway. This approach could be meaningful for glioma given the fact that the median survival following diagnosis of the highest grade of glioma remains short despite current therapy. The identification of new targets for the development of novel therapeutics is therefore needed in order to improve this devastating overall survival rate. This review discusses current literature on translation in gliomas with a focus on the initiation step covering both the cap-dependent and cap-independent modes of initiation. The different translation initiation protagonists will be described in normal conditions and then in gliomas. In addition, their gene expression in gliomas will systematically be examined using two freely available datasets. Finally, we will discuss different pathways regulating translation initiation and current drugs targeting the translational machinery and their potential for the treatment of gliomas.

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Massive Phenotypic Measurements Reveal Complex Physiological Consequences of Differential Translation Efficacies

10.1101/209098 ◽

2017 ◽

Cited By ~ 1

Author(s):

Adam Paul Arkin ◽

Guillaume Cambray

Keyword(s):

Growth Rate ◽

Translation Initiation ◽

Protein Production ◽

Protein Biosynthesis ◽

Cellular Growth ◽

Sequence Variants ◽

Release Rates ◽

Trade Offs ◽

Fluctuating Environments ◽

Protein Overproduction

ABSTRACTControl of protein biosynthesis is at the heart of resource allocation and cell adaptation to fluctuating environments. One gene’s translation often occurs at the expense of another’s, resulting in global energetic and fitness trade-offs during differential expression of various functions. Patterns of ribosome utilization—as controlled by initiation, elongation and release rates—are central to this balance. To disentangle their respective determinants and physiological impacts, we complemented measurements of protein production with highly parallelized quantifications of transcripts’ abundance and decay, ribosome loading and cellular growth rate for 244,000 precisely designed sequence variants of an otherwise standard reporter. We find highly constrained, non-monotonic relationships between measured phenotypes. We show that fitness defects derive either from protein overproduction, with efficient translation initiation and heavy ribosome flows; or from unproductive ribosome sequestration by highly structured, slowly initiated and overly stabilized transcripts. These observations demonstrate physiological impacts of key sequence features in natural and designed transcripts.

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