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The article is devoted to identity construction and self-identification of the protagonist in the film media discourse. Many aspects of our life are influenced by modern media, among which feature films play a significant role. The convergence of visual and auditory channels of perception determines the multi-modal nature of the film media discourse, which in turn contributes to the successful dissemination of the ideas embodied on the screen. The main purpose of the paper is to identify special tactics that are used in film media discourse to demonstrate the stages of the protagonist’s self-identification and identity construction. The research is conducted on the basis of films “Chronicle of amorous accidents” and “Courier”. The multi-modal linguo-semiotic approach is interpreted in the work as a set of linguo-semiotic techniques used in order to study the integrative influence on the viewer’s perception process. It implies the consolidation of functions of human first and second signal systems to construct specific meaning and thus to intervene into the viewers’ cognitive activity. The linguo-semiotic analysis of the data obtained in the study has resulted in the development of an innovative and effective model that demonstrates the existence of a coherent merger of the five tactics and three modes in linguo-cultures. The perspective is a contrasting linguo-semiotic study of the communicative behavior of the protagonists in the modern film media discourse with an emphasis on intercultural differences.

The article examines linguostylistic specifics of the pragmatical and symbolic realization of the poetic discourse based on English. As the purpose of the work, we analyzed the use of linguistic means of symbolization in the English poetic discourse in the linguopragmatic aspect. The article discusses the importance of stylistic means in English for poetic influence on the addressee. In analyzing verses from pragmalinguistic side is necessary to show their stylistic peculiarities. We did a contextual analysis of poetic works at the text and hypotext levels using the method of symbolic interpretation, stylistic analysis, and linguopragmatic analysis. As the material of the study, we analyzed the poetic works of English poets. The theoretical significance of research results is to identify linguistic specifics of pragmatic and symbol realization of the poetic discourse in the English linguoculture. The study contributes to the development of discursive linguistics, pragmalinguistics, lexicology and stylistics of English, theory of linguistics, linguoculturology. In practical terms, results can be used in teaching the theory of discourse, pragmalinguistics, linguistic analysis of the poetic text, lexicology, and stylistics of English.

Introduction Women and men experience sleep differently and the difference in intrinsic desire for sleep might underlie some of the observed male-female differences. The objective of this cross-sectional questionnaire study of university students was to determine male-female differences in self-reported sleepiness and sleep-wake patterns. Methods Five questionnaires were completed by 1650 students at four Russian universities. Results Compared to male students, female students reported a lower subjective sleep quality score, had a higher morning sleepability score and lower nighttime and daytime wakeability scores. They more often reported excessive daytime sleepiness and expected to be sleepier at any time of the day with the largest male-female difference around the times of sleep onset and offset. On free days, they reported a longer sleep duration and an earlier sleep onset. Free-weekday difference was larger for sleep duration and smaller for sleep onset. Such male-female differences showed similarity to the differences observed in university and high school students from different countries around the globe. There was no significant male-female difference in weekly averaged sleep duration, weekday sleep duration, hours slept, midpoint of sleep on free days, free-weekday difference in sleep offset, social jetlag, and morningness-eveningness score. Therefore, when studies rely on these self-reports, the most salient male-female differences might not be immediately evident. Conclusions It seems that the intrinsic desire for longer sleep duration might contribute to a higher susceptibility of female students to weekday sleep loss. Among these students, negative effects of reduced sleep duration might be more common and more detrimental.

Despite recent success in the treatment of hepatocellular carcinoma and other liver cancers, development of new therapeutic approaches remains an unmet medical need. The application of therapeutic nucleic acids allows suppression of complex targets over the long term. Nucleic acid therapeutics can be used either independently or in combination with small molecules and antibodies. Here, we performed design, synthesis and validation of siRNAs targeting gankyrin mRNA in vitro and in vivo. As gankyrin upregulation in hepatocellular carcinoma causes increased proliferation of hepatocytes, gankyrin is a promising therapeutic target. We have shown that the most effective miRNAs are complementary to mRNA fragments that form both single-and double-stranded regions as predicted by modeling of the gankyrin mRNA secondary structure. The most efficient siRNAs were formulated in lipid nanoparticles and showed downregulation of gankyrin mRNA in the murine liver of more than 90% after a single injection of 0.2 mg/kg. Selected siRNAs can be used to study the role of gankyrin in the development of liver cancer and metabolic diseases in murine models.

DDX3 RNA helicase is involved in many processes of RNA metabolism in eukaryotic cells. Many studies of DDX3 have shown that it is also involved in the translation initiation process, both cap-dependent and IRES-dependent. However, the specificity of the secondary structure of mRNA 5'-UTRs, which require DDX3 RNA helicase for effective translation, has not yet been determined. We performed a bioinformatic analysis of the 5'-UTR secondary structures in the pool of DDX3-dependent mRNAs in silico and predicted that the length of 5'-UTRs for such mRNAs is less than the average for the genome and that there are also characteristic hairpin structures in the region of the first 50 nucleotides from the 5'-end of the mRNA.

The practice of realization in the USA and European Union of the parties’ autonomy due to the choice of law, applicable to the cross-border online-contract is explored in the article. Particularly the problems of the choice of law, applicable to the cross-border online-contracts B2B (business to business), B2C (business to consumer) и C2C (consumer to consumer) are analyzed. The question is raised about the fairness of undiscussible clause, considering the choice of law, applicable to the online-contract involving consumers. According to the doctrine, legislation and practice the procedural and constitutive approaches to the solving of this question are observed in the article.

Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation

Long noncoding RNAs (lncRNA) play important roles in the regulation of transcription, splicing, translation, and other processes in the cell. Human and mouse lncRNA (DEANR1 and LL35/Falcor, respectively) located in the genomic environment in close proximity to the Foxa2 transcription factor were discovered earlier. In this work, tissue-specific expression of LL35/Falcor lncRNA has been shown in mouse liver and lungs. The use of antisense oligonucleotides allowed us to achieve LL35/Falcor lncRNA downregulation by 90%. As a result, the level of Foxa2 mRNA and protein dropped, which confirms the involvement of LL35/Falcor lncRNA in the regulation of transcription factor Foxa2. We have shown a decrease in the expression of LL35 lncRNA in liver fibrosis, which correlates with the previously published data for mRNA Foxa2. Thus, lncRNA LL35 regulates Foxa2 expression in the liver not only in normal conditions, but also during development of fibrosis, which allows one to consider lncRNA a biomarker of this pathological process.

Poly(rC)-binding protein 2 (PCBP2, hnRNP E2) is one of the most abundant RNA-binding proteins in mammalian cells. In humans, it exists in seven isoforms, which are assumed to play similar roles in cells. The protein is shown to bind 3′-untranslated regions (3′-UTRs) of many mRNAs and regulate their translation and/or stability, but nothing is known about the functional consequences of PCBP2 binding to 5′-UTRs. Here we show that the PCBP2 isoform f interacts with the 5′-UTRs of mRNAs encoding eIF4G2 (a translation initiation factor with a yet unknown mechanism of action, also known as DAP5) and Cyclin I, and inhibits their translation in vitro and in cultured cells, while the PCBP2 isoform e only affects Cyclin I translation. Furthermore, eIF4G2 participates in a cap-dependent translation of the PCBP2 mRNA. Thus, PCBP2 and eIF4G2 seem to regulate one another's expression via a novel type of feedback loop formed by the translation initiation factor and the RNA-binding protein.

A series of 2′-deoxy and novel 2′-O-methyl and 2′-O-(2-methoxyethyl) (2′-MOE) oligonucleotides with internucleotide methanesulfonyl (mesyl, μ) or 1-butanesulfonyl (busyl, β) phosphoramidate groups has been synthesized for evaluation as potential splice-switching oligonucleotides. Evaluation of their splice-switching activity in spinal muscular atrophy patient-derived fibroblasts revealed no significant difference in splice-switching efficacy between 2′-MOE mesyl oligonucleotide and the corresponding phosphorothioate (nusinersen). Yet, a survival study with model neonatal mice has shown the antisense 2′-MOE mesyl oligonucleotide to be inferior to nusinersen at the highest dose of 40 mg/kg. A reason for their lower activity in vivo as ascertained by cellular uptake study by fluorescent confocal microscopy in HEK293 cell line could possibly be ascribed to compromised endosomal release and/or nuclear uptake of the 2′-OMe or 2′-MOE μ- and β-oligonucleotides compared to their phosphorothioate analog.

The progress of the cell cycle is directly regulated by modulation of cyclins and cyclin-dependent kinases. However, many proteins that control DNA replication, RNA transcription and the synthesis and degradation of proteins can manage the activity or levels of master cell cycle regulators. Among them, RNA helicases are key participants in RNA metabolism involved in the global or specific tuning of cell cycle regulators at the level of transcription and translation. Several RNA helicases have been recently evaluated as promising therapeutic targets, including eIF4A, DDX3 and DDX5. However, targeting RNA helicases can result in side effects due to the influence on the cell cycle. In this review, we discuss direct and indirect participation of RNA helicases in the regulation of the cell cycle in order to draw attention to downstream events that may occur after suppression or inhibition of RNA helicases.

Research on individual differences in the fields of chronobiology and chronopsychology mostly focuses on two – morning and evening – chronotypes. However, recent developments in these fields pointed at a possibility to extend chronotypology beyond just two chronotypes. We examined this possibility by implementing the Single-Item Chronotyping (SIC) as a method for self-identification of chronotype among six simple chart options illustrating the daily change in alertness level. Of 2283 survey participants, 2176 (95%) chose one of these options. Only 13% vs. 24% chose morning vs. evening type (a fall vs. a rise of alertness from morning to evening), while the majority of participants chose four other types (with a peak vs. a dip of alertness in the afternoon and with permanently high vs. low alertness levels throughout the day, 15% vs. 18% and 9% vs. 16%, respectively). The same 6 patterns of diurnal variation in sleepiness were yielded by principal component analysis of sleepiness curves. Six chronotypes were also validated against the assessments of sleep timing, excessive daytime sleepiness, and abilities to wake or sleep on demand at different times of the day. We concluded that the study results supported the feasibility of classification with the 6 options provided by the SIC.

The state of the art in optical biosensing is focused on reaching high sensitivity at a single wavelength by using any type of optical resonance. This common strategy, however, disregards the promising possibility of simultaneous measurements of a bioanalyte’s refractive index over a broadband spectral domain. Here, we address this issue by introducing the approach of in-fibre multispectral optical sensing (IMOS). The operating principle relies on detecting changes in the transmission of a hollow-core microstructured optical fibre when a bioanalyte is streamed through it via liquid cells. IMOS offers a unique opportunity to measure the refractive index at 42 wavelengths, with a sensitivity up to ~3000 nm per refractive index unit (RIU) and a figure of merit reaching 99 RIU−1 in the visible and near-infra-red spectral ranges. We apply this technique to determine the concentration and refractive index dispersion for bovine serum albumin and show that the accuracy meets clinical needs., Optical biosensing: analyzing biological fluids at many wavelengths In-fibre multispectral optical sensing (IMOS) can detect and analyze the optical properties of biological liquids at multiple wavelengths simultaneously, using hollow-core microstructured optical fibres (HC-MOFs). Researchers in Russia and Israel, led by Dmitry Gorin at the Skolkovo Institute of Science and Technology in Moscow and Roman Noskov at Tel Aviv University, developed IMOS and demonstrated its potential using solutions of the bovin serum albumin. IMOS detects changes in the transmission of light in the fibre when the fluid being analyzed flows through the fibre’s hollow core. Refractive index values were measured at 42 wavelength’s of visible and near-infra-red light simultaneously, with potential to measure many more. IMOS is sufficiently accurate for clinical analysis, including detecting the presence and concentration of specific biomolecules in blood. The procedure could supply immediate diagnostic results relevant to a variety of medical conditions, including diabetes and cancer.

The coupling of alternative splicing with the nonsense-mediated decay (NMD) pathway maintains quality control of the transcriptome in eukaryotes by eliminating transcripts with premature termination codons (PTC) and fine-tunes gene expression. Long noncoding RNA (lncRNA) can regulate multiple cellular processes, including alternative splicing. Previously, murine Morrbid (myeloid RNA repressor of Bcl2l11 induced death) lncRNA was described as a locus-specific controller of the lifespan of short-living myeloid cells via transcription regulation of the apoptosis-related Bcl2l11 protein. Here, we report that murine Morrbid lncRNA in hepatocytes participates in the regulation of proto-oncogene NRAS (neuroblastoma RAS viral oncogene homolog) splicing, including the formation of the isoform with PTC. We observed a significant increase of the NRAS isoform with PTC in hepatocytes with depleted Morrbid lncRNA. We demonstrated that the NRAS isoform with PTC is degraded via the NMD pathway. This transcript is presented almost only in the nucleus and has a half-life ~four times lower than other NRAS transcripts. Additionally, in UPF1 knockdown hepatocytes (the key NMD factor), we observed a significant increase of the NRAS isoform with PTC. By a modified capture hybridization (CHART) analysis of the protein targets, we uncovered interactions of Morrbid lncRNA with the SFPQ (splicing factor proline and glutamine rich)-NONO (non-POU domain-containing octamer-binding protein) splicing complex. Finally, we propose the regulation mechanism of NRAS splicing in murine hepatocytes by alternative splicing coupled with the NMD pathway with the input of Morrbid lncRNA.

Ribosome biogenesis is among the founding processes in the cell. During the first stages of ribosome biogenesis, polycistronic precursor of ribosomal RNA passes complex multistage maturation after transcription. Quality control of preribosomal RNA (pre-rRNA) processing is precisely regulated by non-ribosomal proteins and structural features of pre-rRNA molecules, including modified nucleotides. However, many participants of rRNA maturation are still unknown or poorly characterized. We report that RNA m6A methyltransferase Mettl3 interacts with the 5&prime, external transcribed spacer (5&prime, ETS) of the 47S rRNA precursor and modifies adenosine 196. We demonstrated that Mettl3 knockdown results in the increase of pre-rRNA processing rates, while intracellular amounts of rRNA processing machinery components (U3, U8, U13, U14, and U17 small nucleolar RNA (snoRNA )and fibrillarin, nucleolin, Xrn2, and rrp9 proteins), rRNA degradation rates, and total amount of mature rRNA in the cell stay unchanged. Increased efficacy of pre-rRNA cleavage at A&rsquo, and A0 positions led to the decrease of 47S and 45S pre-rRNAs in the cell and increase of mature rRNA amount in the cytoplasm. The newly identified conserved motif DRACH sequence modified by Mettl3 in the 5&prime, ETS region is found and conserved only in primates, which may suggest participation of m6A196 in quality control of pre-rRNA processing at initial stages demanded by increased complexity of ribosome biogenesis.

By means of EEG analysis the functional state of subjects with high and low levels of anxiety was studied in different periods preceding a cognitive task - a visual expression recognition. Several conditions were investigated: background/eyes closed; background/eyes opened; listening the instruction for the cognitive task; operative rest (time lapse between listening the instruction and the beginning of the task), as well as short intervals immediately preceding the exposition of target stimuli (stage of preparation) - pairs of faces pictures with identical or different emotional expressions. At all these pre-task stages high-anxiety subjects exhibited much lower amplitude values in alpha and theta bands (as compared with low-anxiety subjects). The most prominent differences were revealed in the phases of instruction listening and operative rest. These data could provide more precise electrophysiological markers of anxiety level in conditions preceeding cognitive task performance.

The functional state of subjects with high and low levels of anxiety is studied by electroencephalograph analysis of different temporal periods preceding a cognitive task of visual expression recognition. Several conditions are investigated: background/eyes closed; background/eyes opened; listening to instructions for the cognitive task; operative rest (time lapse between listening to instructions and the beginning of the task); as well as short intervals immediately preceding exposure to target stimuli (preparatory stage), which were paired facial images with identical or different emotional expressions. At all these pre-task stages, high-anxiety subjects exhibit much lower electroencephalograph amplitude values for alpha and theta bands (as compared with low-anxiety subjects). The most prominent differences in electroencephalograph amplitude values revealed during the phases of listening to instructions and operative rest. These datum may provide more precise electrophysiological markers of the level of anxiety during conditions preceding cognitive task performance.

Williams-Beuren syndrome is a genetic disorder characterized by physiological and mental abnormalities, and is caused by hemizygous deletion of several genes in chromosome 7. One of the removed genes encodes the WBSCR27 protein. Bioinformatic analysis of the sequence of WBSCR27 indicates that it belongs to the family of SAM-dependent methyltransferases. However, exact cellular functions of this protein or phenotypic consequences of its deficiency are still unknown. Here we report nearly complete 1H, 15N, and 13C chemical shifts assignments of the 26 kDa WBSCR27 protein from Mus musculus in complex with the cofactor S-adenosyl-L-methionine (SAM). Analysis of the assigned chemical shifts allowed us to characterize the protein's secondary structure and backbone dynamics. The topology of the protein's fold confirms the assumption that the WBSCR27 protein belongs to the family of class I methyltransferases.

Proteins containing the NIF3 domain are highly conserved and are found in bacteria, eukaryotes, and archaea. YbgI is an Escherichia coli protein whose gene is conserved among bacteria. The structure of YbgI is known; however, the function of this protein in cells remains obscure. Our studies of E. coli cells with deleted ybgI gene suggest that YbgI is involved in formation of the bacterial cell wall.

DDX3 RNA helicase is intensively studied as a therapeutic target due to participation in the replication of some viruses and involvement in cancer progression. Here we used transcriptome analysis to estimate the primary response of hepatocytes to different levels of RNAi-mediated knockdown of DDX3 RNA helicase both in vitro and in vivo. We found that a strong reduction of DDX3 protein (&gt, 85%) led to similar changes in vitro and in vivo—deregulation of the cell cycle and Wnt and cadherin pathways. Also, we observed the appearance of dead hepatocytes in the healthy liver and a decrease of cell viability in vitro after prolonged treatment. However, more modest downregulation of the DDX3 protein (60–65%) showed discordant results in vitro and in vivo—similar changes in vitro as in the case of strong knockdown and a different phenotype in vivo. These results demonstrate that the level of DDX3 protein can dramatically influence the cell phenotype in vivo and the decrease of DDX3, for more than 85% leads to cell death in normal tissues, which should be taken into account during the drug development of DDX3 inhibitors.

The unique ability of the adult liver to regenerate after injury is the basis for efficient surgical resection and liver transplantation and provides solutions for the treatment of liver cancer and acute liver failure. Current success in surgical treatments could be enhanced by directed regulation of liver regeneration. A number of small molecules and growth factors have been tested in mice models to improve liver regeneration. Noncoding ribonucleic acids (ncRNA) are less studied regulators of various cellular processes. Here, the authors carefully review ncRNA involved in liver regeneration and discuss molecular mechanisms and regulatory networks. These ncRNAs modulate the expression of pro- and antiproliferative genes allowing to orchestrate precisely the proliferation of hepatocytes. The authors expect that ncRNA will become new targets in liver regeneration due to recent progress in therapeutic nucleic acids. Among a large number of preclinical studies on ncRNA, only a few entered clinical trials, and further studies are needed to uncover their potential as therapeutic targets.

В статье представлен опыт ГБОУ СОШ №257 Пушкинского района Санкт-Петербурга по реализации метатем в рамках Опытно-экспериментальной площадки «Проектирование моделей интеграции внеурочной деятельности и дополнительного образования обучающихся в общеобразовательной организации. Показана интеграция на основе метапредметных образовательных проектов и образовательных событий, исследованы реальные проблемы и трудности данного процесса.

Development of multimodal systems for therapy and diagnosis of neoplastic diseases is an unmet need in oncology. The possibility of simultaneous diagnostics, monitoring, and therapy of various diseases allows expanding the applicability of modern systems for drug delivery. We have developed hybrid particles based on biocompatible polymers containing magnetic nanoparticles (MNPs), photoacoustic (MNPs), fluorescent (Cy5 or Cy7 dyes), and therapeutic components (doxorubicin). To achieve high loading efficiency of MNP and Dox to nanostructured carriers, we utilized a novel freezing-induced loading technique. To reduce the systemic toxicity of antitumor drugs and increase their therapeutic efficacy, we can use targeted delivery followed by the remote control of drug release using high intensity-focused ultrasound (HIFU). Loading of MNPs allowed performing magnetic targeting of the carriers and enhanced optoacoustic signal after controlled destruction of the shell and release of therapeutics as well as MRI imaging. The raster scanning optoacoustic mesoscopy (PA, RSOM), MRI, and fluorescent tomography (FT) confirmed the ultrasound-induced release of doxorubicin from capsules: in vitro (in tubes and pieces of meat) and in vivo (after delivery to the liver). Disruption of capsules results in a significant increase of doxorubicin and Cy7 fluorescence initially quenched by magnetite nanoparticles that can be used for real-time monitoring of drug release in vivo. In addition, we explicitly studied cytotoxicity, intracellular localization, and biodistribution of these particles. Elaborated drug delivery carriers have a good perspective for simultaneous imaging and focal therapy of different cancer types, including liver cancer.

In this review we discuss features of mRNA synthesis and modifications used to minimize immune response and prolong efficiency of the translation process in vivo. Considerable attention is given to the use of liposomes and nanoparticles containing lipids and polymers for the mRNA delivery. Finally we briefly discuss mRNAs which are currently in the clinical trials for cancer immunotherapy, vaccination against infectious diseases, and replacement therapy.

Asialoglycoprotein receptor (ASGP-R) is a promising biological target for drug delivery into hepatoma cells. Nevertheless, there are only few examples of small-molecule conjugates of ASGP-R selective ligand equipped by a therapeutic agent for the treatment of hepatocellular carcinoma (HCC). In the present work, we describe a convenient and versatile synthetic approach to novel mono- and multivalent drug-conjugates containing N-acetyl-2-deoxy-2-aminogalactopyranose and anticancer drug - paclitaxel (PTX). Several molecules have demonstrated high affinity towards ASGP-R and good stability under physiological conditions, significant in vitro anticancer activity comparable to PTX, as well as good internalization via ASGP-R-mediated endocytosis. Therefore, the conjugates with the highest potency can be regarded as a promising therapeutic option against HCC.

The ribosome is a macromolecular complex responsible for protein biosynthesis. Two subunits of the bacterial ribosome contain three RNA molecules of more than 4000 nt in total and more than 50 proteins. Ribosome assembly is an intricate multistep process, which is vital for the cell. The review summarizes the current concepts of the mechanisms sustaining bacterial ribosome assembly in the cell and in vitro model systems. Some details of assembling this machine are still unknown.

The possibility of using an S-adenosylmethionine analog, i.e., pent-2-en-4-ynyl S-adenosylhomocysteine (AduEnYn), as an rRNA methyltransferase cofactor has been investigated. The conditions for the cycloaddition reaction of the fluorescent label to the S-adenosylmethionine analog were chosen. The functional activity of E. coli ribosomes was tested under different conditions. It was found that the introduction of the alkynyl radical occurred successfully and did not affect the functional activity of the ribosome; however, the inactivation of the ribosome occurred during the following cycloaddition reaction.

In this work, we report the methodology of studies of the role of bacterial ribosome modifications for regulation of gene expression. A modification of some ribosomal components can affect translation of certain mRNAs. Changes of cellular protein composition caused by deletions of genes responsible for ribosome modifications were detected by proteomic analysis. Using reporter constructs we determined the particular stage of gene expression responsible for variations of protein concentrations. After identification of the mRNA, whose translation was influenced by ribosome modifications, we determined the mRNA regions in the wild-type strain and the strain with unmodified ribosomes responsible for the changes observed. The methodology developed can be applied to studying other translational control mechanisms.

N6-methyladenosine (m(6)A) is ubiquitously present in the RNA of living organisms from Escherichia coli to humans. Methyltransferases that catalyze adenosine methylation are drastically different in specificity from modification of single residues in bacterial ribosomal or transfer RNA to modification of thousands of residues spread among eukaryotic mRNA. Interactions that are formed by m(6)A residues range from RNA-RNA tertiary contacts to RNA-protein recognition. Consequences of the modification loss might vary from nearly negligible to complete reprogramming of regulatory pathways and lethality. In this review, we summarized current knowledge on enzymes that introduce m(6)A modification, ways to detect m(6)A presence in RNA and the functional role of this modification everywhere it is present, from bacteria to humans.

A ribosome is a ribonucleoprotein that performs the synthesis of proteins. Ribosomal RNA of all organisms includes a number of modified nucleotides, such as base or ribose methylated and pseudouridines. Methylated nucleotides are highly conserved in bacteria and some even universally. In this review we discuss available data on a set of modification sites in the most studied bacteria, Escherichia coli. While most rRNA modification enzymes are known for this organism, the function of the modified nucleotides is rarely identified.

The functional centers of the ribosome in all organisms contain ribosomal RNA (rRNA) modifications, which are introduced by specialized enzymes and come at an energy cost for the cell. Surprisingly, none of the modifications tested so far was essential for growth and hence the functional role of modifications is largely unknown. Here, we show that the methyl groups of nucleosides m(2)G966 and m(5)C967 of 16S rRNA in Escherichia coli are important for bacterial fitness. In vitro analysis of all phases of translation suggests that the m(2)G966/m(5)C967 modifications are dispensable for elongation, termination and ribosome recycling. Rather, the modifications modulate the early stages of initiation by stabilizing the binding of fMet-tRNA(fMet) to the 30S pre-initiation complex prior to start-codon recognition. We propose that the m(2)G966 and m(5)C967 modifications help shaping the bacterial proteome, most likely by fine-tuning the rates that determine the fate of a given messenger RNA (mRNA) at early checkpoints of mRNA selection.

Modified nucleosides are present in all kinds of stable RNA molecules, tRNAs being particularly rich in them (Auffinger and Westhof, 1998). Ribosomal RNA (rRNA) from all organisms contains modifications, and there is a correlation between the overall complexity of an organism and the number of modified nucleosides in its rRNA. The rRNA of the most primitive bacteria, such as some Mycoplasma species, may possess only 14 modified nucleosides (de Crecy-Lagard et al., 2007). In Escherichia coli, there are 36 modified nucleosides in rRNA (Table I). Yeast ribosomes possess about one hundred rRNA modifications, human rRNA over two hundred (Ofengand and Fournier, 1998; Decatur and Fournier, 2002). Eukaryotes and archaea use snoRNA guided rRNA modification mechanism. This mechanism allows archaea and eukarya to use a limited number of modification enzymes, mainly pseudouridine synthase and 2′-O-methyltransferase to introduce the majority of their rRNA modifications (Decatur and Fournier, 2002). By contrast, bacteria have developed specific enzymes for each one of the (fewer) modifications they have. Nevertheless, there are many different rRNA modifications in bacteria. Despite intensive study for several decades, many open questions remain regarding the functional role of modified rRNA nucleosides. In this review we will focus on rRNA modifications in E. coli and discuss their possible functions.