Relevant bibliographies by topics / RRNA Recognition

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'RRNA Recognition'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "RRNA Recognition"

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Pilch, Daniel S., Malvika Kaul, Christopher M. Barbieri, and John E. Kerrigan. "Thermodynamics of aminoglycoside-rRNA recognition." Biopolymers 70, no. 1 (August 13, 2003): 58–79. http://dx.doi.org/10.1002/bip.10411.

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Douthwaite, Stephen, Bjørn Voldborg, Lykke Haastrup Hansen, Gunnar Rosendahl, and Birte Vester. "Recognition determinants for proteins and antibiotics within 23S rRNA." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1179–85. http://dx.doi.org/10.1139/o95-127.

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Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination of molecular genetic and biochemical probing techniques, we have concentrated on regions of the rRNA that are connected with specific functions. These are located in different domains within the 23S rRNA and include the ribosomal GTPase-associated center in domain II, which contains the binding sites for r-proteins L10-(L12)4and L11 and is inhibited by interaction with the antibiotic thiostrepton. The peptidyltransferase center within domain V is inhibited by macrolide, lincosamide, and streptogramin B antibiotics, which interact with the rRNA around nucleotide A2058. Drug resistance is conferred by mutations here and by modification of A2058 by ErmE methyltransferase. ErmE recognizes a conserved motif displayed in the primary and secondary structure of the peptidyl transferase loop. Within domain VI of the rRNA, the α-sarcin stem–loop is associated with elongation factor binding and is the target site for ribotoxins including the N-glycosidase ribosome-inactivating proteins ricin and pokeweed antiviral protein (PAP). The orientations of the 23S rRNA domains are constrained by tertiary interactions, including a pseudoknot in domain II and long-range base pairings in the center of the molecule that bring domains II and V closer together. The phenotypic effects of mutations in these regions have been investigated by expressing 23S rRNA from plasmids. Allele-specific priming sites have been introduced close to these structures in the rRNA to enable us to study the molecular events there.Key words: rRNA tertiary structure, rRNA–antibiotic interaction, r-protein binding, Erm methyltransferase, rRNA modification.
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Fukai, S., O. Nureki, S. Sekine, A. Shimada, Dmitry Vassylyev, and S. Yokoyama. "Recognition mechanism of valine tRNA by valyl-rRNA synthetase." Seibutsu Butsuri 41, supplement (2001): S183. http://dx.doi.org/10.2142/biophys.41.s183_1.

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Rodgers, Margaret L., Yunsheng Sun, and Sarah A. Woodson. "Ribosomal Protein S12 Hastens Nucleation of Co-Transcriptional Ribosome Assembly." Biomolecules 13, no. 6 (June 6, 2023): 951. http://dx.doi.org/10.3390/biom13060951.

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Ribosomal subunits begin assembly during transcription of the ribosomal RNA (rRNA), when the rRNA begins to fold and associate with ribosomal proteins (RPs). In bacteria, the first steps of ribosome assembly depend upon recognition of the properly folded rRNA by primary assembly proteins such as S4, which nucleates assembly of the 16S 5′ domain. Recent evidence, however, suggests that initial recognition by S4 is delayed due to variable folding of the rRNA during transcription. Here, using single-molecule colocalization co-transcriptional assembly (smCoCoA), we show that the late-binding RP S12 specifically promotes the association of S4 with the pre-16S rRNA during transcription, thereby accelerating nucleation of 30S ribosome assembly. Order of addition experiments suggest that S12 helps chaperone the rRNA during transcription, particularly near the S4 binding site. S12 interacts transiently with the rRNA during transcription and, consequently, a high concentration is required for its chaperone activity. These results support a model in which late-binding RPs moonlight as RNA chaperones during transcription in order to facilitate rapid assembly.
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Nosrati, Meisam, Debayan Dey, Atousa Mehrani, Sarah E. Strassler, Natalia Zelinskaya, Eric D. Hoffer, Scott M. Stagg, Christine M. Dunham, and Graeme L. Conn. "Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition." Journal of Biological Chemistry 294, no. 46 (October 8, 2019): 17642–53. http://dx.doi.org/10.1074/jbc.ra119.011181.

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Methylation of the small ribosome subunit rRNA in the ribosomal decoding center results in exceptionally high-level aminoglycoside resistance in bacteria. Enzymes that methylate 16S rRNA on N7 of nucleotide G1405 (m7G1405) have been identified in both aminoglycoside-producing and clinically drug-resistant pathogenic bacteria. Using a fluorescence polarization 30S-binding assay and a new crystal structure of the methyltransferase RmtC at 3.14 Å resolution, here we report a structure-guided functional study of 30S substrate recognition by the aminoglycoside resistance-associated 16S rRNA (m7G1405) methyltransferases. We found that the binding site for these enzymes in the 30S subunit directly overlaps with that of a second family of aminoglycoside resistance-associated 16S rRNA (m1A1408) methyltransferases, suggesting that both groups of enzymes may exploit the same conserved rRNA tertiary surface for docking to the 30S. Within RmtC, we defined an N-terminal domain surface, comprising basic residues from both the N1 and N2 subdomains, that directly contributes to 30S-binding affinity. In contrast, additional residues lining a contiguous adjacent surface on the C-terminal domain were critical for 16S rRNA modification but did not directly contribute to the binding affinity. The results from our experiments define the critical features of m7G1405 methyltransferase–substrate recognition and distinguish at least two distinct, functionally critical contributions of the tested enzyme residues: 30S-binding affinity and stabilizing a binding-induced 16S rRNA conformation necessary for G1405 modification. Our study sets the scene for future high-resolution structural studies of the 30S-methyltransferase complex and for potential exploitation of unique aspects of substrate recognition in future therapeutic strategies.
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Gerstner, Resi B., Yong Pak, and David E. Draper. "Recognition of 16S rRNA by Ribosomal Protein S4 fromBacillus stearothermophilus†." Biochemistry 40, no. 24 (June 2001): 7165–73. http://dx.doi.org/10.1021/bi010026i.

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Lebars, Isabelle, Clotilde Husson, Satoko Yoshizawa, Stephen Douthwaite, and Dominique Fourmy. "Recognition Elements in rRNA for the Tylosin Resistance Methyltransferase RlmAII." Journal of Molecular Biology 372, no. 2 (September 2007): 525–34. http://dx.doi.org/10.1016/j.jmb.2007.06.068.

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8

Signorino, Giacomo, Nastaran Mohammadi, Francesco Patanè, Marco Buscetta, Mario Venza, Isabella Venza, Giuseppe Mancuso, et al. "Role of Toll-Like Receptor 13 in Innate Immune Recognition of Group B Streptococci." Infection and Immunity 82, no. 12 (September 15, 2014): 5013–22. http://dx.doi.org/10.1128/iai.02282-14.

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ABSTRACTMurine Toll-like receptor 13 (TLR13), an endosomal receptor that is not present in humans, is activated by an unmethylated motif present in the large ribosomal subunit of bacterial RNA (23S rRNA). Little is known, however, of the impact of TLR13 on antibacterial host defenses. Here we examined the role of this receptor in the context of infection induced by the model pathogen group B streptococcus (GBS). To this end, we used bacterial strains masked from TLR13 recognition by virtue of constitutive expression of the ErmC methyltransferase, which results in dimethylation of the 23S rRNA motif at a critical adenine residue. We found that TLR13-mediated rRNA recognition was required for optimal induction of tumor necrosis factor alpha and nitrous oxide in dendritic cell and macrophage cultures stimulated with heat-killed bacteria or purified bacterial RNA. However, TLR13-dependent recognition was redundant when live bacteria were used as a stimulus. Moreover, masking bacterial rRNA from TLR13 recognition did not increase the ability of GBS to avoid host defenses and replicatein vivo. In contrast, increased susceptibility to infection was observed under conditions in which signaling by all endosomal TLRs was abolished, i.e., in mice with a loss-of-function mutation in the chaperone protein UNC93B1. Our data lend support to the conclusion that TLR13 participates in GBS recognition, although blockade of the function of this receptor can be compensated for by other endosomal TLRs. Lack of selective pressure by bacterial infections might explain the evolutionary loss of TLR13 in humans. However, further studies using different bacterial species are needed to prove this hypothesis.
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Kaul, Malvika, and Daniel S. Pilch. "Thermodynamics of Aminoglycoside−rRNA Recognition: The Binding of Neomycin-Class Aminoglycosides to the A Site of 16S rRNA†." Biochemistry 41, no. 24 (June 2002): 7695–706. http://dx.doi.org/10.1021/bi020130f.

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PEREDERINA, ANNA, NATALIA NEVSKAYA, OLEG NIKONOV, ALEXEI NIKULIN, PHILIPPE DUMAS, MIN YAO, ISAO TANAKA, MARIA GARBER, GEORGE GONGADZE, and STANISLAV NIKONOV. "Detailed analysis of RNA–protein interactions within the bacterial ribosomal protein L5/5S rRNA complex." RNA 8, no. 12 (December 2002): 1548–57. http://dx.doi.org/10.1017/s1355838202029953.

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The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 Å resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA–protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the β-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.
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Dissertations / Theses on the topic "RRNA Recognition"

1

Punekar, Avinash S. "Ribosomal RNA Modification Enzymes : Structural and functional studies of two methyltransferases for 23S rRNA modification in Escherichia coli." Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212394.

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Escherichia coli ribosomal RNA (rRNA) is post-transcriptionally modified by site-specific enzymes. The role of most modifications is not known and little is known about how these enzymes recognize their target substrates. In this thesis, we have structurally and functionally characterized two S-adenosyl-methionine (SAM) dependent 23S rRNA methyltransferases (MTases) that act during the early stages of ribosome assembly in E. coli. RlmM methylates the 2'O-ribose of C2498 in 23S rRNA. We have solved crystal structures of apo RlmM at 1.9Å resolution and of an RlmM-SAM complex at 2.6Å resolution. The RlmM structure revealed an N-terminal THUMP domain and a C-terminal catalytic Rossmann-fold MTase domain. A continuous patch of conserved positive charge on the RlmM surface is likely used for RNA substrate recognition. The SAM-binding site is open and shallow, suggesting that the RNA substrate may be required for tight cofactor binding. Further, we have shown RlmM MTase activity on in vitro transcribed 23S rRNA and its domain V. RlmJ methylates the exocyclic N6 atom of A2030 in 23S rRNA. The 1.85Å crystal structure of RlmJ revealed a Rossmann-fold MTase domain with an inserted small subdomain unique to the RlmJ family. The 1.95Å structure of the RlmJ-SAH-AMP complex revealed that ligand binding induces structural rearrangements in the four loop regions surrounding the active site. The active site of RlmJ is similar to N6-adenine DNA MTases. We have shown RlmJ MTase activity on in vitro transcribed 23S rRNA and a minimal substrate corresponding to helix 72, specific for adenosine. Mutagenesis experiments show that residues Y4, H6, K18 and D164 are critical for catalytic activity. These findings have furthered our understanding of the structure, evolution, substrate recognition and mechanism of rRNA MTases.
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Book chapters on the topic "RRNA Recognition"

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Zheng, Zejun, Thuy-Diem Nguyen, and Bertil Schmidt. "CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA." In Pattern Recognition in Bioinformatics, 37–49. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-24855-9_4.

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Vázquez-González, Lara, Carlos Peña-Reyes, Carlos Balsa-Castro, Inmaculada Tomás, and María J. Carreira. "An Ensemble-Based Phenotype Classifier to Diagnose Crohn’s Disease from 16s rRNA Gene Sequences." In Pattern Recognition and Image Analysis, 557–68. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-36616-1_44.

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Conference papers on the topic "RRNA Recognition"

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Rushforth, Alex, Marta Sienkiewicsz, Haley Hazlett, Ruth Schmidt, Sarah de Rijcke, and Stephen Curry. "Introducing RRA-Tracker: An online tool mapping the global research assessment reform landscape." In 27th International Conference on Science, Technology and Innovation Indicators (STI 2023). International Conference on Science, Technology and Innovation Indicators, 2023. http://dx.doi.org/10.55835/6439616d4e3bac8a15a26df3.

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Over the past decade, international efforts to reform how research is recognized and rewarded in academia have gathered substantial momentum. Animated by concerns that overly-narrow criteria and indicators of research quality are creating unsustainable and unequal career systems and narrowing knowledge production, various reform movements focusing on responsible metrics, research integrity, open research, Diversity, Equity and Inclusion have coalesced under the label of Responsible Research Assessment (RRA). Reform of research assessment remains a challenging process because it impacts established processes, cultures and norms. Despite the growing recognition of the need for change, organisations embarking on reform programmes may not always be sure where is the best place to start. The RRA-Tracker aims to help them overcome that hesitancy. The RRA-Tracker is an online tool for exploring how academic research institutions around the world have introduced and implemented new responsible research assessment practices. The tool enables more experienced institutions to share what they are doing with the wider world, while helping other institutions gain an overview of global developments in assessment reform. It’s populated with policies, roadmaps and other documents from hundreds of institutions all over the world covering innovations in academic hiring, promotion and tenure assessments, together with expertly curated insights to help users discover and discuss what’s possible. This poster presentation will introduce the RRA-Tracker, describing its origins, the co-creation process behind it, current coverage and scope, and potential for further development. It will provide screenshots of the tool, as well as QR codes linking the STI audience directly to the tool.
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Ullah, Asad, Jing Wang, M. Shahid Anwar, Usman Ahmad, Jin Wang, and Uzair Saeed. "Nonlinear Manifold Feature Extraction Based on Spectral Supervised Canonical Correlation Analysis for Facial Expression Recognition with RRNN." In 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI). IEEE, 2018. http://dx.doi.org/10.1109/cisp-bmei.2018.8633244.

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