Eukaryotic rRNA are modified frequently, although the diversity of modifications is low: in yeast rRNA, there are only 12 different types out of a possible natural repertoire exceeding 112. All nine ...rRNA base methyltransferases (MTases) and one acetyltransferase have recently been identified in budding yeast, and several instances of crosstalk between rRNA, tRNA, and mRNA modifications are emerging. Although the machinery has largely been identified, the functions of most rRNA modifications remain to be established. Remarkably, a eukaryote-specific bridge, comprising a single ribosomal protein (RP) from the large subunit (LSU), contacts four rRNA base modifications across the ribosomal subunit interface, potentially probing for their presence. We hypothesize in this article that long-range allosteric communication involving rRNA modifications is taking place between the two subunits during translation or, perhaps, the late stages of ribosome assembly.
All nine rRNA base methyltransferases have been identified in budding yeast.
An 18S rRNA acetyltransferase modifies tRNAs with a specific adaptor.
Four methyltransferases are stabilized by a common coactivator.
A eukaryote-specific bridge monitors base modifications across the subunit interface.
rRNAs are extensively modified during their transcription and subsequent maturation in the nucleolus, nucleus and cytoplasm. RNA modifications, which are installed either by snoRNA-guided or by ...stand-alone enzymes, generally stabilize the structure of the ribosome. However, they also cluster at functionally important sites of the ribosome, such as the peptidyltransferase center and the decoding site, where they facilitate efficient and accurate protein synthesis. The recent identification of sites of substoichiometric 2′-O-methylation and pseudouridylation has overturned the notion that all rRNA modifications are constitutively present on ribosomes, highlighting nucleotide modifications as an important source of ribosomal heterogeneity. While the mechanisms regulating partial modification and the functions of specialized ribosomes are largely unknown, changes in the rRNA modification pattern have been observed in response to environmental changes, during development, and in disease. This suggests that rRNA modifications may contribute to the translational control of gene expression.
Yeast 25S rRNA was reported to contain a single cytosine methylation (m(5)C). In the present study using a combination of RP-HPLC, mung bean nuclease assay and rRNA mutagenesis, we discovered that ...instead of one, yeast contains two m(5)C residues at position 2278 and 2870. Furthermore, we identified and characterized two putative methyltransferases, Rcm1 and Nop2 to be responsible for these two cytosine methylations, respectively. Both proteins are highly conserved, which correlates with the presence of two m(5)C residues at identical positions in higher eukaryotes, including humans. The human homolog of yeast Nop2, p120 has been discovered to be upregulated in various cancer tissues, whereas the human homolog of Rcm1, NSUN5 is completely deleted in the William's-Beuren Syndrome. The substrates and function of both human homologs remained unknown. In the present study, we also provide insights into the significance of these two m(5)C residues. The loss of m(5)C2278 results in anisomycin hypersensitivity, whereas the loss of m(5)C2870 affects ribosome synthesis and processing. Establishing the locations and enzymes in yeast will not only help identifying the function of their homologs in higher organisms, but will also enable understanding the role of these modifications in ribosome function and architecture.
N
-acetylcytidine (ac
C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA
. However, the distribution, ...dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac
C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac
C at single-nucleotide resolution. In human and yeast mRNAs, ac
C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac
C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac
C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac
C and its potential thermoadaptive role. Our studies quantitatively define the ac
C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease
.
Magnetic nanoparticles (MNPs) owing to its broad application spectrum are gaining popularity in recent years. The current review article offers a one-stop-reference for young scientists as it ...encompasses the literature reports on method of synthesis and functionalization of MNPs based systems and their potential applications spectrum in diverse fields. This review summarizes in details about different methods reported in literature for the synthesis of MNPs, need of functionalization of MNPs, immobilization of active species onto the surface of functionalized MNPs and their applications in carrying out biologically important organic transformation. Applications of MNPs are not only restricted to the field of catalysis but also showed potential applications in different sectors. Over the last few decades, there has been increasing global concern over public health issues due to contamination of water bodies with harmful dyes and toxic metals. Monitoring and subsequent removal of these harmful dyes and toxic metals from the contaminated water is one of the major environmental remediation interests today. In this context, MNPs based absorbents have shown exuberant potential to remove deleterious pollutants from water bodies owing to their high removal efficiency, low cost, faster kinetics, easy accessibility and design flexibility. Besides, MNPs have also proved their potential in the field of enzyme and pharmaceutical industries. MNPs being the major class of nanoscale materials are revolutionizing the current clinical diagnostic and therapeutic techniques and are currently employed as next generation drug carriers. Furthermore, Magnetic NP-Based Biosensors was also employed for detection of the presence of SARS-CoV-2, a ribonucleic acid (RNA) virus responsible for nearly 6.1 million deaths occurred due to COVID-19 pandemic. MNPs based system also showed their potential in fuel industry as it is used in the production of biodiesel which emerges as a promising alternative to fossil fuel derived energy sources because it is eco-friendly, clean and biodegradable in nature. In short, we have provided in-depth details about the MNPs, their synthesis, functionalization and their applications in diverse fields.
Graphical abstract captain: Functionalized MNPs and their diverse application spectrumMNPs based catalytic systems have revolutionized the modern era. They have indispensable application spectrum not only in synthetic chemistry but have shown their significant impact in pharmaceuticals, contaminants removal, and enzymatic industry among others. Display omitted
•MNPs based catalytic systems are non-toxic and ecofriendly.•Functionalized MNPs have indispensable merits over conventional supports.•MNPs based systems have multifaceted application spectrum in synthetic chemistry, pharmaceutical industry, enzymatic industry etc. among others.•MNPs are revolutionizing the current clinical diagnostic and therapeutic sectors.•MNPs based systems are utilized in the treatment of water bodies•MNPs based system used for biodiesel production•MNPs as biosensors
The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5'-end capped RNAs is now well established. Nevertheless, the biological function of this nucleotide metabolite cap remains ...elusive. Here, we show that the yeast Saccharomyces cerevisiae cytoplasmic 5'-end exoribonuclease Xrn1 is also a NAD cap decapping (deNADding) enzyme that releases intact NAD and subsequently degrades the RNA. The significance of Xrn1 deNADding is evident in a deNADding deficient Xrn1 mutant that predominantly still retains its 5'-monophosphate exonuclease activity. This mutant reveals Xrn1 deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and may influence intramitochondrial NAD levels. Our findings uncover a contribution of mitochondrial NAD-capped RNAs in overall NAD regulation with the deNADding activity of Xrn1 fulfilling a central role.
This paper reports a 10-bit 150 MS/s successive approximation register analog-to-digital converter with binary-scaled redundancy-facilitated error correction technique. The proposed 1.5-bit/cycle ...technique with built-in capacitive digital-to-analog converter (CDAC) redundancy, corrects multiple erroneous decisions in a total of nine conversion cycles. The proposed binary-scaled redundancy provides a 12.5% error tolerance range for the incomplete CDAC voltage settling. The digital error-correction logic circuit presented uses a bit-overlap-and-add technique. The prototype chip was fabricated in 65-nm CMOS technology and occupies chip area of 0.038 mm 2 . It consumes 4.06 mW from a 1.2 V supply, achieving the Nyquist signal-to-noise-and-distortion ratio of 57.81 dB and the effective number of bits of 9.31-bit at an operating frequency of 150 MS/s, corresponding to the figure-of-merit of 42.6 fJ/ conversion-step.
Ribosomes are essential nanomachines responsible for protein production. Although ribosomes are present in every living cell, ribosome biogenesis dysfunction diseases, called ribosomopathies, impact ...particular tissues specifically. Here, we evaluate the importance of the box C/D snoRNA-associated ribosomal RNA methyltransferase fibrillarin (Fbl) in the early embryonic development of Xenopus laevis. We report that in developing embryos, the neural plate, neural crest cells (NCCs), and NCC derivatives are rich in fbl transcripts. Fbl knockdown leads to striking morphological defects affecting the eyes and craniofacial skeleton, due to lack of NCC survival caused by massive p53-dependent apoptosis. Fbl is required for efficient pre-rRNA processing and 18S rRNA production, which explains the early developmental defects. Using RiboMethSeq, we systematically reinvestigated ribosomal RNA 2'-O methylation in X. laevis, confirming all 89 previously mapped sites and identifying 15 novel putative positions in 18S and 28S rRNA. Twenty-three positions, including 10 of the new ones, were validated orthogonally by low dNTP primer extension. Bioinformatic screening of the X. laevis transcriptome revealed candidate box C/D snoRNAs for all methylated positions. Mapping of 2'-O methylation at six developmental stages in individual embryos indicated a trend towards reduced methylation at specific positions during development. We conclude that fibrillarin knockdown in early Xenopus embryos causes reduced production of functional ribosomal subunits, thus impairing NCC formation and migration.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Several pathways modulating longevity and stress resistance converge on translation by targeting ribosomal proteins or initiation factors, but whether this involves modifications of ribosomal RNA is ...unclear. Here, we show that reduced levels of the conserved RNA methyltransferase NSUN5 increase the lifespan and stress resistance in yeast, worms and flies. Rcm1, the yeast homologue of NSUN5, methylates C2278 within a conserved region of 25S rRNA. Loss of Rcm1 alters the structural conformation of the ribosome in close proximity to C2278, as well as translational fidelity, and favours recruitment of a distinct subset of oxidative stress-responsive mRNAs into polysomes. Thus, rather than merely being a static molecular machine executing translation, the ribosome exhibits functional diversity by modification of just a single rRNA nucleotide, resulting in an alteration of organismal physiological behaviour, and linking rRNA-mediated translational regulation to modulation of lifespan, and differential stress response.
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. ...Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs-snR4 and snR45 -not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs. We show that base pairing between these snoRNAs and 18S rRNA requires the putative helicase activity of Kre33, which is also needed to aid early pre-rRNA processing. Compared to yeast, the number of orphan box C/D snoRNAs in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
PDF
