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Molecular Regulation and Mechanism of Ribonucleoprotein Complexes

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 25230

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Dr. Elena A Stolboushkina

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Guest Editor

Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
Interests: ribosomes; biogenesis; cryo-EM; cryo-electron microscopy

Special Issue Information

Dear Colleagues,

Ribonucleoprotein сomplexes (RNP) are essential in all cellular life forms: Bacteria, Archaea, Eukaryotes and even in non-cellular infectious agents – RNA viruses. Ribonucleoprotein сomplexes consist of ribonucleic acids and RNA-binding proteins. There are huge RNP complexes such as RNA viruses, vault complex, ribosome, spliceosome, heterogeneous ribonucleoprotein particles (hnRNP) and smaller ones: telomerase, replicase, RNase P, aminoacyl-tRNA synthetases etc. These complexes have important biological roles in replication of RNA viruses, cellular transcription and translation, post-transcriptional and post- translational modification and also regulation of these processes. For the Special Issue "Molecular Regulation and Mechanism of Ribonucleoprotein Complexes" of the International Journal of Molecular Sciences we accept original research manuscripts and reviews highlighting different structural and functional aspects of any ribonucleoprotein сomplex. We are interested the recent advances in the area of structural organization, mechanisms of function, assembly and transport RNPs, and also regulation of processes involving ones. The knowledge and understanding of these fundamental processes is essential for the fight against aging, genetic diseases and antibiotic resistance, for improving anticancer drugs and an antiviral therapy (especially topical for COVID-19).

Dr. Elena A Stolboushkina
Guest Editor

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Keywords

ribonucleoprotein сomplexes (RNP)
RNA viruses, vault complex, ribosome
spliceosome
heterogeneous ribonucleoprotein particles (hnRNP)
telomerase
replicase
RNase P
aminoacyl-tRNA synthetases

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Published Papers (10 papers)

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Research

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20 pages, 4172 KiB

Open AccessArticle

Human Tissues Exhibit Diverse Composition of Translation Machinery

by Aleksandra S. Anisimova, Natalia M. Kolyupanova, Nadezhda E. Makarova, Artyom A. Egorov, Ivan V. Kulakovskiy and Sergey E. Dmitriev

Int. J. Mol. Sci. 2023, 24(9), 8361; https://doi.org/10.3390/ijms24098361 - 6 May 2023

Cited by 5 | Viewed by 2667

Abstract

While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas, we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g., PABP and eRF3 paralogs, eIF2B and eIF3 subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified the testis and brain as organs with the most diverged expression of translation-associated genes. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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12 pages, 2686 KiB

Open AccessArticle

Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases

by Ananya Das, Nichole Adiletta and Dmitri N. Ermolenko

Int. J. Mol. Sci. 2023, 24(8), 6878; https://doi.org/10.3390/ijms24086878 - 7 Apr 2023

Viewed by 1946

Abstract

Translational G proteins, whose release from the ribosome is triggered by GTP hydrolysis, regulate protein synthesis. Concomitantly with binding and dissociation of protein factors, translation is accompanied by forward and reverse rotation between ribosomal subunits. Using single-molecule measurements, we explore the ways in which the binding of translational GTPases affects inter-subunit rotation of the ribosome. We demonstrate that the highly conserved translation factor LepA, whose function remains debated, shifts the equilibrium toward the non-rotated conformation of the ribosome. By contrast, the catalyst of ribosome translocation, elongation factor G (EF-G), favors the rotated conformation of the ribosome. Nevertheless, the presence of P-site peptidyl-tRNA and antibiotics, which stabilize the non-rotated conformation of the ribosome, only moderately reduces EF-G binding. These results support the model suggesting that EF-G interacts with both the non-rotated and rotated conformations of the ribosome during mRNA translocation. Our results provide new insights into the molecular mechanisms of LepA and EF-G action and underscore the role of ribosome structural dynamics in translation. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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14 pages, 2290 KiB

Open AccessArticle

The RNA-Binding and RNA-Melting Activities of the Multifunctional Protein Nucleobindin 1

by Alisa Mikhaylina, Arina Svoeglazova, Elena Stolboushkina, Svetlana Tishchenko and Olga Kostareva

Int. J. Mol. Sci. 2023, 24(7), 6193; https://doi.org/10.3390/ijms24076193 - 24 Mar 2023

Cited by 1 | Viewed by 1471

Abstract

Nucleobindin 1 (NUCB1) is a ubiquitous multidomain protein that belongs to the EF-hand Ca²⁺-binding superfamily. NUCB1 interacts with Galpha_i3 protein, cyclooxygenase, amyloid precursor protein, and lipids. It is involved in stress response and human diseases. In addition, this protein is a transcription factor that binds to the DNA E-box motif. Using surface plasmon resonance and molecular beacon approaches, we first showed the RNA binding and RNA melting activities of NUCB1. We suggest that NUCB1 could induce local changes in structured RNAs via binding to the GG

\frac{A}{U} \frac{A}{U}

loop sequence. Our results demonstrate the importance of the multidomain structure of NUCB1 for its RNA-chaperone activity in vitro. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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16 pages, 3487 KiB

Open AccessArticle

Purification and Characterization of Authentic 30S Ribosomal Precursors Induced by Heat Shock

by Emmanuel Giudice, Sylvie Georgeault, Régis Lavigne, Charles Pineau, Annie Trautwetter, Gwennola Ermel, Carlos Blanco and Reynald Gillet

Int. J. Mol. Sci. 2023, 24(4), 3491; https://doi.org/10.3390/ijms24043491 - 9 Feb 2023

Viewed by 2275

Abstract

Ribosome biogenesis is a complex and multistep process that depends on various assembly factors. To understand this process and identify the ribosome assembly intermediates, most studies have set out to delete or deplete these assembly factors. Instead, we took advantage of the impact of heat stress (45 °C) on the late stages of the biogenesis of the 30S ribosomal subunit to explore authentic precursors. Under these conditions, reduced levels of the DnaK chaperone proteins devoted to ribosome assembly lead to the transient accumulation of 21S ribosomal particles, which are 30S precursors. We constructed strains with different affinity tags on one early and one late 30S ribosomal protein and purified the 21S particles that form under heat shock. A combination of relative quantification using mass spectrometry-based proteomics and cryo-electron microscopy (cryo-EM) was then used to determine their protein contents and structures. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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18 pages, 2507 KiB

Open AccessArticle

Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro

by Julia Svetlova, Ekaterina Knizhnik, Valentin Manuvera, Vyacheslav Severov, Dmitriy Shirokov, Ekaterina Grafskaia, Pavel Bobrovsky, Elena Matyugina, Anastasia Khandazhinskaya, Liubov Kozlovskaya, Nataliya Miropolskaya, Andrey Aralov, Yuri Khodarovich, Vladimir Tsvetkov, Sergey Kochetkov, Vassili Lazarev and Anna Varizhuk

Int. J. Mol. Sci. 2022, 23(23), 15281; https://doi.org/10.3390/ijms232315281 - 3 Dec 2022

Cited by 6 | Viewed by 2259

Abstract

The life cycle of severe acute respiratory syndrome coronavirus 2 includes several steps that are supposedly mediated by liquid–liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and genomic RNA. To facilitate the rational design of LLPS-targeting therapeutics, we modeled N-RNA biomolecular condensates in vitro and analyzed their sensitivity to several small-molecule antivirals. The model condensates were obtained and visualized under physiological conditions using an optimized RNA sequence enriched with N-binding motifs. The antivirals were selected based on their presumed ability to compete with RNA for specific N sites or interfere with non-specific pi–pi/cation–pi interactions. The set of antivirals included fleximers, 5′-norcarbocyclic nucleoside analogs, and perylene-harboring nucleoside analogs as well as non-nucleoside amphiphilic and hydrophobic perylene derivatives. Most of these antivirals enhanced the formation of N-RNA condensates. Hydrophobic perylene derivatives and 5′-norcarbocyclic derivatives caused up to 50-fold and 15-fold enhancement, respectively. Molecular modeling data argue that hydrophobic compounds do not hamper specific N-RNA interactions and may promote non-specific ones. These findings shed light on the determinants of potent small-molecule modulators of viral LLPS. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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18 pages, 1928 KiB

Open AccessArticle

The HIV-1 Integrase C-Terminal Domain Induces TAR RNA Structural Changes Promoting Tat Binding

by Cecilia Rocchi, Camille Louvat, Adriana Erica Miele, Julien Batisse, Christophe Guillon, Lionel Ballut, Daniela Lener, Matteo Negroni, Marc Ruff, Patrice Gouet and Francesca Fiorini

Int. J. Mol. Sci. 2022, 23(22), 13742; https://doi.org/10.3390/ijms232213742 - 8 Nov 2022

Cited by 6 | Viewed by 2219

Abstract

Recent evidence indicates that the HIV-1 Integrase (IN) binds the viral genomic RNA (gRNA), playing a critical role in the morphogenesis of the viral particle and in the stability of the gRNA once in the host cell. By combining biophysical, molecular biology, and biochemical approaches, we found that the 18-residues flexible C-terminal tail of IN acts as a sensor of the peculiar apical structure of the trans-activation response element RNA (TAR), interacting with its hexaloop. We show that the binding of the whole IN C-terminal domain modifies TAR structure, exposing critical nucleotides. These modifications favour the subsequent binding of the HIV transcriptional trans-activator Tat to TAR, finally displacing IN from TAR. Based on these results, we propose that IN assists the binding of Tat to TAR RNA. This working model provides a mechanistic sketch accounting for the emerging role of IN in the early stages of proviral transcription and could help in the design of anti-HIV-1 therapeutics against this new target of the viral infectious cycle. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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18 pages, 6906 KiB

Open AccessArticle

Functional Interactions of Kluyveromyces lactis Telomerase Reverse Transcriptase with the Three-Way Junction and the Template Domains of Telomerase RNA

by Wasif Al-Shareef, Yogev Brown, Christopher Bryan, Elena Shuvaeva, Shhadeh Bsoul, Raanan Greenman, Majdi M. Kabaha, Nikolai B. Ulyanov, Emmanuel Skordalakes and Yehuda Tzfati

Int. J. Mol. Sci. 2022, 23(18), 10757; https://doi.org/10.3390/ijms231810757 - 15 Sep 2022

Cited by 1 | Viewed by 1555

Abstract

The ribonucleoprotein telomerase contains two essential components: telomerase RNA (TER) and telomerase reverse transcriptase (TERT, Est2 in yeast). A small portion of TER, termed the template, is copied by TERT onto the chromosome ends, thus compensating for sequence loss due to incomplete DNA replication and nuclease action. Although telomerase RNA is highly divergent in sequence and length across fungi and mammals, structural motifs essential for telomerase function are conserved. Here, we show that Est2 from the budding yeast Kluyveromyces lactis (klEst2) binds specifically to an essential three-way junction (TWJ) structure in K. lactis TER, which shares a conserved structure and sequence features with the essential CR4-CR5 domain of vertebrate telomerase RNA. klEst2 also binds specifically to the template domain, independently and mutually exclusive of its interaction with TWJ. Furthermore, we present the high-resolution structure of the klEst2 telomerase RNA-binding domain (klTRBD). Mutations introduced in vivo in klTRBD based on the solved structure or in TWJ based on its predicted RNA structure caused severe telomere shortening. These results demonstrate the conservation and importance of these domains and the multiple protein–RNA interactions between Est2 and TER for telomerase function. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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17 pages, 4657 KiB

Open AccessArticle

RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin

by Tinashe P. Maviza, Anastasiia S. Zarechenskaia, Nadezhda R. Burmistrova, Andrey S. Tchoub, Olga A. Dontsova, Petr V. Sergiev and Ilya A. Osterman

Int. J. Mol. Sci. 2022, 23(12), 6453; https://doi.org/10.3390/ijms23126453 - 9 Jun 2022

Cited by 2 | Viewed by 4056

Abstract

In the bid to survive and thrive in an environmental setting, bacterial species constantly interact and compete for resources and space in the microbial ecosystem. Thus, they have adapted to use various antibiotics and toxins to fight their rivals. Simultaneously, they have evolved an ability to withstand weapons that are directed against them. Several bacteria harbor colicinogenic plasmids which encode toxins that impair the translational apparatus. One of them, colicin E3 ribotoxin, mediates cleavage of the 16S rRNA in the decoding center of the ribosome. In order to thrive upon deployment of such ribotoxins, competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. A recent study demonstrated the role of PrfH and the RtcB2 module in rescuing a damaged ribosome and the subsequent re-ligation of the cleaved 16S rRNA by colicin E3 in vitro. The rtcB2-prfH genes coexist as gene neighbors in an operon that is sporadically spread among different bacteria. In the current study, we report that the RtcB2-PrfH module confers resistance to colicin E3 toxicity in E. coli ATCC25922 cells in vivo. We demonstrated that the viability of E. coli ATCC25922 strain that is devoid of rtcB2 and prfH genes is impaired upon action of colicin E3, in contrast to the parental strain which has intact rtcB2 and prfH genes. Complementation of the rtcB2 and prfH gene knockout with a high copy number-plasmid (encoding either rtcB2 alone or both rtcB2-prfH operon) restored resistance to colicin E3. These results highlight a counter-conflict system that may have evolved to thwart colicin E3 activity. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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Review

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34 pages, 2675 KiB

Open AccessReview

Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres

by Nikita Shepelev, Olga Dontsova and Maria Rubtsova

Int. J. Mol. Sci. 2023, 24(5), 5027; https://doi.org/10.3390/ijms24055027 - 6 Mar 2023

Cited by 3 | Viewed by 3175

Abstract

Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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12 pages, 795 KiB

Open AccessReview

Elusive Trans-Acting Factors Which Operate with Type I (Poliovirus-like) IRES Elements

by Dmitry E. Andreev, Michael Niepmann and Ivan N. Shatsky

Int. J. Mol. Sci. 2022, 23(24), 15497; https://doi.org/10.3390/ijms232415497 - 7 Dec 2022

Cited by 3 | Viewed by 2113

Abstract

The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5′ untranslated region (5′UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity. Full article

(This article belongs to the Special Issue Molecular Regulation and Mechanism of Ribonucleoprotein Complexes)

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