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Journal articles on the topic 'RRNA Recognition'

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Author: Grafiati
Published: 6 September 2023

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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9

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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10

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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11

Parameswaran, Preethi, Yashaswina Arora, Rajesh Patidar, and Nihar Ranjan. "Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding." Biophysical Chemistry 274 (July 2021): 106589. http://dx.doi.org/10.1016/j.bpc.2021.106589.

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12

Bao, Hongyu, Na Wang, Chongyuan Wang, Yiyang Jiang, Jiuyang Liu, Li Xu, Jihui Wu, and Yunyu Shi. "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Research 45, no. 20 (October 3, 2017): 12005–14. http://dx.doi.org/10.1093/nar/gkx872.

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13

Korobeinikova, A. V., G. M. Gongadze, A. P. Korepanov, B. D. Eliseev, M. V. Bazhenova, and M. B. Garber. "5S rRNA-recognition module of CTC family proteins and its evolution." Biochemistry (Moscow) 73, no. 2 (February 2008): 156–63. http://dx.doi.org/10.1134/s0006297908020065.

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14

Ross, Wilma, Sarah E. Aiyar, Julia Salomon, and Richard L. Gourse. "Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters." Journal of Bacteriology 180, no. 20 (October 15, 1998): 5375–83. http://dx.doi.org/10.1128/jb.180.20.5375-5383.1998.

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ABSTRACT The α subunit of Escherichia coli RNA polymerase (RNAP) participates in promoter recognition through specific interactions with UP element DNA, a region upstream of the recognition hexamers for the ς subunit (the −10 and −35 hexamers). UP elements have been described in only a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promoter activity. Here, we analyzed the effects of upstream sequences from several additional E. coli promoters (rrnD P1, rrnB P2, λp R, lac, merT, and RNA II). The relative effects of different upstream sequences were compared in the context of their own core promoters or as hybrids to thelac core promoter. Different upstream sequences had different effects, increasing transcription from 1.5- to ∼90-fold, and several had the properties of UP elements: they increased transcription in vitro in the absence of accessory protein factors, and transcription stimulation required the C-terminal domain of the RNAP α subunit. The effects of the upstream sequences correlated generally with their degree of similarity to an UP element consensus sequence derived previously. Protection of upstream sequences by RNAP in footprinting experiments occurred in all cases and was thus not a reliable indicator of UP element strength. These data support a modular view of bacterial promoters in which activity reflects the composite effects of RNAP interactions with appropriately spaced recognition elements (−10, −35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.
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15

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (May 1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260-2272.1992.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.
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16

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (May 1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.
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17

Thanaraj, T. A., A. S. Kolaskar, and M. W. Pandit. "Prediction of the Recognition Sites on 16S and 23S rRNAs fromE.colifor the Formation of 16S-23S rRNA Complex." Journal of Biomolecular Structure and Dynamics 6, no. 3 (December 1988): 587–92. http://dx.doi.org/10.1080/07391102.1988.10506509.

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18

ARIFIN, UMILAELA, DJOKO T. ISKANDAR, DAVID P. BICKFORD, RAFE M. BROWN, RUDOLF MEIER, and SUJATHA NARAYANAN KUTTY. "Phylogenetic relationships within the genus Staurois (Anura, Ranidae) based on 16S rRNA sequences." Zootaxa 2744, no. 1 (January 19, 2011): 39. http://dx.doi.org/10.11646/zootaxa.2744.1.3.

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We estimate the phylogenetic relationships among all six recognized species of the genus Staurois based on 16S rRNA sequences (~522 bp) for 92 specimens from Borneo and the Philippines. Our preferred phylogenetic tree inferred from Maximum Parsimony and Bayesian methods reveal six major clades within the genus leading to recognition of S. natator, S. nubilus, S. guttatus, S. tuberilinguis, S. parvus, and S. latopalmatus. For species where multiple populations were assessed, we found high genetic variation that may eventually support the recognition of new species.
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19

Chen, XiaoZhou. "A New Signal Segmemtation Algorithm for Recognition of 23S rRNA Structual Domains." Procedia Engineering 15 (2011): 1509–13. http://dx.doi.org/10.1016/j.proeng.2011.08.280.

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20

NIELSEN, ALLAN K., STEPHEN DOUTHWAITE, and BIRTE VESTER. "Negative in vitro selection identifies the rRNA recognition motif for ErmE methyltransferase." RNA 5, no. 8 (August 1999): 1034–41. http://dx.doi.org/10.1017/s1355838299990349.

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21

Wang, Xiaojing, Michael T. Migawa, Kristin A. Sannes-Lowery, and Eric E. Swayze. "The synthesis and 16S A-site rRNA recognition of carbohydrate-free aminoglycosides." Bioorganic & Medicinal Chemistry Letters 15, no. 22 (November 2005): 4919–22. http://dx.doi.org/10.1016/j.bmcl.2005.08.027.

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22

Rowe, Sebastian J., Ryan J. Mecaskey, Mohamed Nasef, Rachel C. Talton, Rory E. Sharkey, Joshua C. Halliday, and Jack A. Dunkle. "Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition." Journal of Biological Chemistry 295, no. 51 (October 5, 2020): 17476–85. http://dx.doi.org/10.1074/jbc.ra120.014280.

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Erythromycin-resistance methyltransferases are SAM dependent Rossmann fold methyltransferases that convert A2058 of 23S rRNA to m62A2058. This modification sterically blocks binding of several classes of antibiotics to 23S rRNA, resulting in a multidrug-resistant phenotype in bacteria expressing the enzyme. ErmC is an erythromycin resistance methyltransferase found in many Gram-positive pathogens, whereas ErmE is found in the soil bacterium that biosynthesizes erythromycin. Whether ErmC and ErmE, which possess only 24% sequence identity, use similar structural elements for rRNA substrate recognition and positioning is not known. To investigate this question, we used structural data from related proteins to guide site-saturation mutagenesis of key residues and characterized selected variants by antibiotic susceptibility testing, single turnover kinetics, and RNA affinity–binding assays. We demonstrate that residues in α4, α5, and the α5-α6 linker are essential for methyltransferase function, including an aromatic residue on α4 that likely forms stacking interactions with the substrate adenosine and basic residues in α5 and the α5-α6 linker that likely mediate conformational rearrangements in the protein and cognate rRNA upon interaction. The functional studies led us to a new structural model for the ErmC or ErmE-rRNA complex.
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23

Head, Kelly, Koichi S. Kobayashi, Michael F. Criscitiello, and Saptha Vijayan. "Demonstration of TLR response in O. mykiss by the bacterial 23S rRNA motif." Journal of Immunology 202, no. 1_Supplement (May 1, 2019): 190.61. http://dx.doi.org/10.4049/jimmunol.202.supp.190.61.

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Abstract The innate immune system is designed to recognize conserved pathogenic sequences known as pathogen-associated molecular patterns (PAMPs), and it is through the modification of these PAMPs that pathogens can subvert innate immune mechanisms. The target of this study is a conserved motif in the bacterial 23S rRNA, which demonstrates a reduced ability to mutate due to lethality to the organism from degraded ribosomal function. The detection of this motif through the pattern recognition receptor (PRR) TLR13 was demonstrated to elicit an immune response across eight animal phyla and Protistan amoeba phyla through this receptor or its orthologs. In teleost fish, the representative model rainbow trout (Oncorhynchus mykiss) was used to study 23S rRNA recognition by TLR22 and TLR13 initiation of an immune response.
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24

Henry, Kemardo K., Wilma Ross, Kevin S. Myers, Kimberly C. Lemmer, Jessica M. Vera, Robert Landick, Timothy J. Donohue, and Richard L. Gourse. "A majority ofRhodobacter sphaeroidespromoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation." Proceedings of the National Academy of Sciences 117, no. 47 (November 9, 2020): 29658–68. http://dx.doi.org/10.1073/pnas.2010087117.

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Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacteriumRhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription fromR. sphaeroidesrRNA promoters was unexpectedly weak, correlating with absence of −7T, the very highly conserved thymine found at the last position in −10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position −7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating thatR. sphaeroidesRNAP can utilize −7T when present. rRNA promoters were activated by purifiedR. sphaeroidesCarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 nativeR. sphaeroidespromoters tested in vitro that lacked −7T, whereas it had no effect on three of the four native promoters that contained −7T. Genome-wide bioinformatic analysis of promoters fromR. sphaeroidesand two other α-proteobacterial species indicated that 30 to 43% contained −7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained −7T. Thus, promoters lacking −7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction inR. sphaeroidesCarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.
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25

Corrêa, Laís L., Marta A. Witek, Natalia Zelinskaya, Renata C. Picão, and Graeme L. Conn. "Heterologous Expression and Functional Characterization of the Exogenously Acquired Aminoglycoside Resistance Methyltransferases RmtD, RmtD2, and RmtG." Antimicrobial Agents and Chemotherapy 60, no. 1 (November 9, 2015): 699–702. http://dx.doi.org/10.1128/aac.02482-15.

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ABSTRACTThe exogenously acquired 16S rRNA methyltransferases RmtD, RmtD2, and RmtG were cloned and heterologously expressed inEscherichia coli, and the recombinant proteins were purified to near homogeneity. Each methyltransferase conferred an aminoglycoside resistance profile consistent with m7G1405 modification, and this activity was confirmed byinvitro30S methylation assays. Analyses of protein structure and interaction withS-adenosyl-l-methionine suggest that the molecular mechanisms of substrate recognition and catalysis are conserved across the 16S rRNA (m7G1405) methyltransferase family.
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26

Beumer, Amy, and Jayne B. Robinson. "A Broad-Host-Range, Generalized Transducing Phage (SN-T) Acquires 16S rRNA Genes from Different Genera of Bacteria." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8301–4. http://dx.doi.org/10.1128/aem.71.12.8301-8304.2005.

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ABSTRACT Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing phages (D3112, UT1, and SN-T), but not specialized transducing phages (D3), acquired entire bacterial 16S rRNA genes. Furthermore, we show that the broad-host-range, generalized transducing phage SN-T is capable of acquiring the 16S rRNA gene from two different genera: Sphaerotilus natans, the host from which SN-T was originally isolated, and Pseudomonas aeruginosa. In sequential infections, SN-T harbored only 16S rRNA gene sequences of the final host as determined by restriction fragment length polymorphism analysis. The frequency of 16S rRNA gene sequences in SN-T populations was determined to be 1 × 10−9 transductants/PFU. Our findings further implicate transduction in the horizontal transfer of 16S rRNA genes between different species or genera of bacteria.
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27

Russell, I. D., and D. Tollervey. "NOP3 is an essential yeast protein which is required for pre-rRNA processing." Journal of Cell Biology 119, no. 4 (November 15, 1992): 737–47. http://dx.doi.org/10.1083/jcb.119.4.737.

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The four nucleolar proteins NOP1, SSB1, GAR1, and NSR1 of Saccharomyces cerevisiae share a repetitive domain composed of repeat units rich in glycine and arginine (GAR domain). We have cloned and sequenced a fifth member of this family, NOP3, and shown it to be essential for cell viability. The NOP3 open reading frame encodes a 415 amino acid protein with a predicted molecular mass of 45 kD, containing a GAR domain and an RNA recognition motif. NOP3-specific antibodies recognize a 60-kD protein by SDS-PAGE and decorate the nucleolus and the surrounding nucleoplasm. A conditional lethal mutation, GAL::nop3, was constructed; growth of the mutant strain in glucose medium represses NOP3 expression. In cells depleted of NOP3, production of cytoplasmic ribosomes is impaired. Northern analysis and pulse-chase labeling indicate that pre-rRNA processing is inhibited at the late steps, in which 27SB pre-rRNA is cleaved to 25S rRNA and 20S pre-rRNA to 18S rRNA.
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28

Correll, Carl C., Betty Freeborn, Peter B. Moore, and Thomas A. Steitz. "Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain." Cell 91, no. 5 (November 1997): 705–12. http://dx.doi.org/10.1016/s0092-8674(00)80457-2.

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29

Wang, Lei, Martin Ciganda, and Noreen Williams. "Defining the RNA-Protein Interactions in the Trypanosome Preribosomal Complex." Eukaryotic Cell 12, no. 4 (February 8, 2013): 559–66. http://dx.doi.org/10.1128/ec.00004-13.

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ABSTRACT In eukaryotes, 5S rRNA is transcribed in the nucleoplasm and requires the ribosomal protein L5 to deliver it to the nucleolus for ribosomal assembly. The trypanosome-specific proteins P34 and P37 form a novel preribosomal complex with the eukaryotic conserved L5-5S rRNA complex in the nucleoplasm. Previous results suggested that P34 acts together with L5 to bridge the interaction with 5S rRNA and thus to stabilize 5S rRNA, an important role in the early steps of ribosomal biogenesis. Here, we have delineated the domains of the two protein components, L5 and P34, and regions of the RNA partner, 5S rRNA, that are critical for protein-RNA interactions within the complex. We found that the L18 domain of L5 and the N terminus and RNA recognition motif of P34 bind 5S rRNA. We showed that Trypanosoma brucei L5 binds the β arm of 5S rRNA, while P34 binds loop A/stem V of 5S rRNA. We demonstrated that 5S rRNA is able to enhance the association between the protein components of the complex, L5 and P34. Both loop A/stem V and the β arm of 5S rRNA can separately enhance the protein-protein association, but their effects are neither additive nor synergistic. Domains in the two proteins for protein-protein and protein-RNA interactions overlap or are close to each other. This suggests that 5S rRNA binding might cause conformational changes in L5 and P34 and might also bridge the interactions, thus enhancing binding between the protein partners of this novel complex.
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30

Clarridge, Jill E. "Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases." Clinical Microbiology Reviews 17, no. 4 (October 2004): 840–62. http://dx.doi.org/10.1128/cmr.17.4.840-862.2004.

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SUMMARY The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.
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31

Lee, W. C., D. Zabetakis, and T. Mélèse. "NSR1 is required for pre-rRNA processing and for the proper maintenance of steady-state levels of ribosomal subunits." Molecular and Cellular Biology 12, no. 9 (September 1992): 3865–71. http://dx.doi.org/10.1128/mcb.12.9.3865-3871.1992.

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NSR1 is a yeast nuclear localization sequence-binding protein showing striking similarity in its domain structure to nucleolin. Cells lacking NSR1 are viable but have a severe growth defect. We show here that NSR1, like nucleolin, is involved in ribosome biogenesis. The nsr1 mutant is deficient in pre-rRNA processing such that the initial 35S pre-rRNA processing is blocked and 20S pre-rRNA is nearly absent. The reduced amount of 20S pre-rRNA leads to a shortage of 18S rRNA and is reflected in a change in the distribution of 60S and 40S ribosomal subunits; there is no free pool of 40S subunits, and the free pool of 60S subunits is greatly increased in size. The lack of free 40S subunits or the improper assembly of these subunits causes the nsr1 mutant to show sensitivity to the antibiotic paromomycin, which affects protein translation, at concentrations that do not affect the growth of the wild-type strain. Our data support the idea that NSR1 is involved in the proper assembly of pre-rRNA particles, possibly by bringing rRNA and ribosomal proteins together by virtue of its nuclear localization sequence-binding domain and multiple RNA recognition motifs. Alternatively, NSR1 may also act to regulate the nuclear entry of ribosomal proteins required for proper assembly of pre-rRNA particles.
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32

Lee, W. C., D. Zabetakis, and T. Mélèse. "NSR1 is required for pre-rRNA processing and for the proper maintenance of steady-state levels of ribosomal subunits." Molecular and Cellular Biology 12, no. 9 (September 1992): 3865–71. http://dx.doi.org/10.1128/mcb.12.9.3865.

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NSR1 is a yeast nuclear localization sequence-binding protein showing striking similarity in its domain structure to nucleolin. Cells lacking NSR1 are viable but have a severe growth defect. We show here that NSR1, like nucleolin, is involved in ribosome biogenesis. The nsr1 mutant is deficient in pre-rRNA processing such that the initial 35S pre-rRNA processing is blocked and 20S pre-rRNA is nearly absent. The reduced amount of 20S pre-rRNA leads to a shortage of 18S rRNA and is reflected in a change in the distribution of 60S and 40S ribosomal subunits; there is no free pool of 40S subunits, and the free pool of 60S subunits is greatly increased in size. The lack of free 40S subunits or the improper assembly of these subunits causes the nsr1 mutant to show sensitivity to the antibiotic paromomycin, which affects protein translation, at concentrations that do not affect the growth of the wild-type strain. Our data support the idea that NSR1 is involved in the proper assembly of pre-rRNA particles, possibly by bringing rRNA and ribosomal proteins together by virtue of its nuclear localization sequence-binding domain and multiple RNA recognition motifs. Alternatively, NSR1 may also act to regulate the nuclear entry of ribosomal proteins required for proper assembly of pre-rRNA particles.
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33

Hager, Jutta, Bart L. Staker, and Ursula Jakob. "Substrate Binding Analysis of the 23S rRNA Methyltransferase RrmJ." Journal of Bacteriology 186, no. 19 (October 1, 2004): 6634–42. http://dx.doi.org/10.1128/jb.186.19.6634-6642.2004.

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ABSTRACT The 23S rRNA methyltransferase RrmJ (FtsJ) is responsible for the 2′-O methylation of the universally conserved U2552 in the A loop of 23S rRNA. This 23S rRNA modification appears to be critical for ribosome stability, because the absence of functional RrmJ causes the cellular accumulation of the individual ribosomal subunits at the expense of the functional 70S ribosomes. To gain insight into the mechanism of substrate recognition for RrmJ, we performed extensive site-directed mutagenesis of the residues conserved in RrmJ and characterized the mutant proteins both in vivo and in vitro. We identified a positively charged, highly conserved ridge in RrmJ that appears to play a significant role in 23S rRNA binding and methylation. We provide a structural model of how the A loop of the 23S rRNA binds to RrmJ. Based on these modeling studies and the structure of the 50S ribosome, we propose a two-step model where the A loop undocks from the tightly packed 50S ribosomal subunit, allowing RrmJ to gain access to the substrate nucleotide U2552, and where U2552 undergoes base flipping, allowing the enzyme to methylate the 2′-O position of the ribose.
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34

Janse, Ingmar, W. Edwin A. Kardinaal, Marion Meima, Jutta Fastner, Petra M. Visser, and Gabriel Zwart. "Toxic and Nontoxic Microcystis Colonies in Natural Populations Can Be Differentiated on the Basis of rRNA Gene Internal Transcribed Spacer Diversity." Applied and Environmental Microbiology 70, no. 7 (July 2004): 3979–87. http://dx.doi.org/10.1128/aem.70.7.3979-3987.2004.

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ABSTRACT Assessing and predicting bloom dynamics and toxin production by Microcystis requires analysis of toxic and nontoxic Microcystis genotypes in natural communities. We show that genetic differentiation of Microcystis colonies based on rRNA internal transcribed spacer (ITS) sequences provides an adequate basis for recognition of microcystin producers. Consequently, ecological studies of toxic and nontoxic cyanobacteria are now possible through studies of rRNA ITS genotypic diversity in isolated cultures or colonies and in natural communities. A total of 107 Microcystis colonies were isolated from 15 lakes in Europe and Morocco, the presence of microcystins in each colony was examined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and they were grouped by rRNA ITS denaturing gradient gel electrophoresis (DGGE) typing. Based on DGGE analysis of amplified ITSa and ITSc fragments, yielding supplementary resolution (I. Janse et al., Appl. Environ. Microbiol. 69:6634-6643, 2003), the colonies could be differentiated into 59 classes. Microcystin-producing and non-microcystin-producing colonies ended up in different classes. Sequences from the rRNA ITS of representative strains were congruent with the classification based on DGGE and confirmed the recognition of microcystin producers on the basis of rRNA ITS. The rRNA ITS sequences also confirmed inconsistencies reported for Microcystis identification based on morphology. There was no indication for geographical restriction of strains, since identical sequences originated from geographically distant lakes. About 28% of the analyzed colonies gave rise to multiple bands in DGGE profiles, indicating either aggregation of different colonies, or the occurrence of sequence differences between multiple operons. Cyanobacterial community profiles from two Dutch lakes from which colonies had been isolated showed different relative abundances of genotypes between bloom stages and between the water column and surface scum. Although not all bands in the community profiles could be matched with isolated colonies, the profiles suggest a dominance of nontoxic colonies, mainly later in the season and in scums.
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35

Luo, Jiaoyang, Dan Yan, Da Zhang, Yumei Han, Xiaoping Dong, Yong Yang, Kejun Deng, and Xiaohe Xiao. "Application of 12S rRNA Barcodes for the Identification of Animal-Derived Drugs." Journal of Pharmacy & Pharmaceutical Sciences 14, no. 3 (September 9, 2011): 358. http://dx.doi.org/10.18433/j3n017.

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Purpose. Animal-derived drugs are the major source of biological products and traditional medicine, but they are often difficult to identify, causing confusion in the clinical application. Among these medicinal animals, a number of animal species are endangered, leading to the destruction of biodiversity. The identification of animal-derived drugs and their alternatives would be a first step toward biodiversity conservation and safe medication. Until now, no effective method for identifying animal-derived drugs has been demonstrated; DNA-based species identification presents a brand-new technique. Methods. We designed primers to amplify a 523-bp fragment of 12S rRNA and generated sequences for 13 individuals within six medicinal animal species. We examined the efficiency of species recognition based on this sequence, and we also tested the taxonomic affiliations against the GenBank database. Results. All the tested drugs were identified successfully, and a visible gap was found between the inter-specific and intra-specific variation. We further demonstrated the importance of data exploration in DNA-based species identification practice by examining the sequence characteristics of relative genera in GenBank. This region of the 12S rRNA gene had a 100% success rate of species recognition within the six medicinal animal species. Conclusions. We propose that the 12S rRNA locus might be universal for identifying animal-derived drugs and their adulterants. The development of 12S rRNA for indentifying animal-derived drugs that share a common gene target would contribute significantly to the clinical application of animal-derived drugs and the conservation of medicinal animal species. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.
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36

Learned, R. M., S. Cordes, and R. Tjian. "Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I." Molecular and Cellular Biology 5, no. 6 (June 1985): 1358–69. http://dx.doi.org/10.1128/mcb.5.6.1358-1369.1985.

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A whole-cell HeLa extract was fractionated into two components required for accurate in vitro transcription of human rRNA. One fraction contained endogenous RNA polymerase I, and the second component contained a factor (SL1) that confers promoter selectivity to RNA polymerase I. Analysis of mutant templates suggests that the core control element of the rRNA promoter is required for activation of transcription by SL1. We purified SL1 approximately 100,000-fold by column chromatography and have shown that the addition of SL1 can reprogram the otherwise nonpermissive mouse transcription system to recognize and initiate accurate RNA synthesis from human rDNA. Antibodies raised against SL1 bind preferentially to a protein localized in the nucleolus of primate cells and specifically inhibit in vitro transcription initiating from the human rRNA promoter. By contrast, anti-SL1 does not react with the nucleolus of rodent cells and has no effect on the in vitro synthesis of mouse rRNA by a transcription system derived from mouse cells. These findings suggest that SL1 is a selectivity factor present in the nucleolus that imparts promoter recognition to RNA polymerase I and that can discriminate between rRNA promoters from different species.
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37

Learned, R. M., S. Cordes, and R. Tjian. "Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I." Molecular and Cellular Biology 5, no. 6 (June 1985): 1358–69. http://dx.doi.org/10.1128/mcb.5.6.1358.

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A whole-cell HeLa extract was fractionated into two components required for accurate in vitro transcription of human rRNA. One fraction contained endogenous RNA polymerase I, and the second component contained a factor (SL1) that confers promoter selectivity to RNA polymerase I. Analysis of mutant templates suggests that the core control element of the rRNA promoter is required for activation of transcription by SL1. We purified SL1 approximately 100,000-fold by column chromatography and have shown that the addition of SL1 can reprogram the otherwise nonpermissive mouse transcription system to recognize and initiate accurate RNA synthesis from human rDNA. Antibodies raised against SL1 bind preferentially to a protein localized in the nucleolus of primate cells and specifically inhibit in vitro transcription initiating from the human rRNA promoter. By contrast, anti-SL1 does not react with the nucleolus of rodent cells and has no effect on the in vitro synthesis of mouse rRNA by a transcription system derived from mouse cells. These findings suggest that SL1 is a selectivity factor present in the nucleolus that imparts promoter recognition to RNA polymerase I and that can discriminate between rRNA promoters from different species.
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38

Derz, Kerstin, Ulrich Klinner, Ingolf Schuphan, Erko Stackebrandt, and Reiner M. Kroppenstedt. "Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species." International Journal of Systematic and Evolutionary Microbiology 54, no. 6 (November 1, 2004): 2313–17. http://dx.doi.org/10.1099/ijs.0.03003-0.

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The taxonomic position of a polycyclic-aromatic-hydrocarbon-degrading bacterium, strain 17A3T, isolated from contaminated soil was determined using a combination of phenotypic and genotypic properties. The isolate showed phenotypic properties that were diagnostic for species of the genus Mycobacterium. Comparative 16S rRNA gene sequence analysis assigned 17A3T to the 16S rRNA gene subgroup that contains Mycobacterium aurum, Mycobacterium austroafricanum, Mycobacterium vaccae and Mycobacterium vanbaalenii, but it could clearly be distinguished from these species using a combination of physiological, chemotaxonomic markers and internal rRNA gene spacer analyses. The data showed that strain 17A3T (=DSM 44605T=NRRL B-24244T) merits recognition as the type strain of a novel species of the genus Mycobacterium. The name Mycobacterium pyrenivorans sp. nov. is proposed for the species because of its ability to use pyrene as a sole source of carbon and energy.
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39

Chu, J. L., N. Brot, H. Weissbach, and K. Elkon. "Lupus antiribosomal P antisera contain antibodies to a small fragment of 28S rRNA located in the proposed ribosomal GTPase center." Journal of Experimental Medicine 174, no. 3 (September 1, 1991): 507–14. http://dx.doi.org/10.1084/jem.174.3.507.

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The ribosomal P proteins are necessary for GTPase activity during protein synthesis. In addition to antibodies to the P proteins, sera from lupus patients contain anti-rRNA activity. To determine whether lupus antiribosomal sera recognize the region of 28S rRNA recently proposed to form part of the ribosomal GTPase center, an rRNA fragment corresponding to nucleotides (nt) 1922-2020 was transcribed in vitro and tested for antigenicity. 18 of 24 (75%) lupus sera containing anti-P antibodies, but only 2 of 24 (8%) lupus sera without anti-P, immunoprecipitated this rRNA fragment (p less than 0.001). The binding was specific, since no significant differences were observed between anti-P positive and negative lupus sera in binding to the RNA fragment transcribed in the antisense orientation or to a control region of rRNA. The majority of sera tested protected a rRNA fragment of approximately 68 nucleotides. To evaluate the fine specificity of the anti-28S antibodies, deletions and site-directed mutations were made in the RNA fragment. The anti-28S antisera required nt 1944-1955 for recognition and were remarkably sensitive to destabilizing as well as nondestabilizing mutations in the stems of the RNA fragments. Detection of antiprotein and anti-RNA antibodies directed against a functionally related domain in the ribosome, together with the remarkable specificity of anti-28S antibodies, strongly suggests a direct role for this region of the ribosome in initiating and/or maintaining antiribosomal autoantibody production.
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40

Baneth, Gad, John R. Barta, Varda Shkap, Donald S. Martin, Douglass K. Macintire, and Nancy Vincent-Johnson. "Genetic and Antigenic Evidence Supports the Separation of Hepatozoon canis and Hepatozoon americanum at the Species Level." Journal of Clinical Microbiology 38, no. 3 (2000): 1298–301. http://dx.doi.org/10.1128/jcm.38.3.1298-1301.2000.

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Recognition of Hepatozoon canis and Hepatozoon americanum as distinct species was supported by the results of Western immunoblotting of canine anti-H. canis and anti-H. americanum sera against H. canisgamonts. Sequence analysis of 368 bases near the 3′ end of the 18S rRNA gene from each species revealed a pairwise difference of 13.59%.
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41

Aykut, Yilmaz. "The importance in DNA barcoding of the regions which is covering rRNA genes and its sequences in the genus Quercus L." Bangladesh Journal of Plant Taxonomy 27, no. 2 (December 11, 2020): 261–71. http://dx.doi.org/10.3329/bjpt.v27i2.50666.

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Turkey with 18 oak (Quercus) species is one of the richest country according to species number and diversity. The most important reason of the species diversity in Turkey is its location and geomorphological structure which increase climatic effects and seperate Turkey into different phytogeographic regions. Furthermore, hybridization behaviours which frequently observed between oak species, genetic drift, gene flow and ecological factors cause morphological variations in the plants species. All of these factors make it difficult to define the species concept for plant groups like oaks. Therefore, the region covering 18S rRNA gene/ ITS1/ 5.8S rRNA gene/ ITS2/ 25S rRNA gene and secondly intergenic spacer (IGS)/ 5S rRNA gene for barcoding were obtained from genbank and used as a useful tool for the determination and solution of the phylogenetic relations of taxonomically problematic species, also these barcoding regions were compared with each other according to species recognition ability for oak species. As a result, it can be stated that both barcoding regions have high variable sites based on sequence information to identify the species and evaluate relationships of species studied. Bangladesh J. Plant Taxon. 27(2): 261-271, 2020 (December)
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42

Pan, Wen-An, Hsin-Yue Tsai, Shun-Chang Wang, Michael Hsiao, Pei-Yu Wu, and Ming-Daw Tsai. "The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression." RNA Biology 12, no. 3 (March 4, 2015): 255–67. http://dx.doi.org/10.1080/15476286.2015.1017221.

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43

Masquida, Benoît, Brice Felden, and Eric Westhof. "Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core." Bioorganic & Medicinal Chemistry 5, no. 6 (June 1997): 1021–35. http://dx.doi.org/10.1016/s0968-0896(97)00053-9.

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44

Tillault, Anne-Sophie, Sarah K. Schultz, Hans-Joachim Wieden, and Ute Kothe. "Molecular Determinants for 23S rRNA Recognition and Modification by the E. coli Pseudouridine Synthase RluE." Journal of Molecular Biology 430, no. 9 (April 2018): 1284–94. http://dx.doi.org/10.1016/j.jmb.2018.03.011.

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45

Lu, Ming, and David E. Draper. "On the role of rRNA tertiary structure in recognition of ribosomal protein L11 and thiostrepton." Nucleic Acids Research 23, no. 17 (1995): 3426–33. http://dx.doi.org/10.1093/nar/23.17.3426.

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46

Kvist, Sebastian, Christopher E. Laumer, Juan Junoy, and Gonzalo Giribet. "New insights into the phylogeny, systematics and DNA barcoding of Nemertea." Invertebrate Systematics 28, no. 3 (2014): 287. http://dx.doi.org/10.1071/is13061.

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Although some clades of ribbon worms (phylum Nemertea) are consistently recovered with high support in molecular phylogenies, the placement and inter-relationships of some taxa have proven problematic. Herein, we performed molecular phylogenetic analyses aimed at resolving these recalcitrant splits, using six loci (nuclear 18S rRNA, 28S rRNA, histones H3 and H4, and mitochondrial 16S rRNA and COI) for 133 terminals, with particular emphasis on the problematic families Hubrechtidae and Plectonemertidae. Three different datasets were used for phylogenetic analyses and both maximum likelihood and maximum parsimony methodologies were applied. All but one of the resulting tree topologies agree on the paraphyly of the class Palaeonemertea, whereas Heteronemertea, Hoplonemertea, Polystilifera, Monostilifera and Hubrechtidae are always recovered as reciprocally monophyletic. Hubrechtidae is sister group to Heteronemertea (the Pilidiophora hypothesis) only when length variable regions of 18S rRNA and 28S rRNA are excluded. Moreover, the terrestrial and freshwater family Plectonemertidae is recovered with high support and the implications of this finding are further discussed. Finally, we evaluate the utility of DNA barcoding for specimen identification within Nemertea using an extended dataset containing 394 COI sequences. Results suggest that DNA barcoding may work for Nemertea, insofar as a distinct barcoding gap (the gap between the maximum intraspecific variation and the minimum interspecific divergence) may exist, but its recognition is regularly hampered by low accuracy in species level identifications.
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47

Ehresmann, Chantal, Claude Philippe, E. Westhof, Bernard Ehresmann, Lionel Bénard, and Claude Portier. "A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1131–40. http://dx.doi.org/10.1139/o95-122.

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Escherichia coli ribosomal protein S15 down regulates its own synthesis by binding to its mRNA in a region overlapping the ribosome binding site, called the translational operator. This binding stabilizes a pseudoknot structure that exists in equilibrium with two stem–loop structures. When synthesized in excess over 16S rRNA, S15 binds to its translational operator and traps the ribosome on its loading site in a transient state, preventing the formation of the active ternary (30S–mRNA–rRNAfMet) complex. This inhibition can be suppressed by 16S rRNA, which displaces S15 from the mRNA. An extensive mutational analysis showed that the pseudoknot is the structural element required for S15 recognition and in vivo translational control. Specific sequence determinants are located in limited regions of the structure formed by the pseudoknot. An unexpected result is that the pseudoknot can exist in a variety of topologically equivalent structures recognizable and shapable by S15. Based on footprinting experiments and computer graphic modelling, S15 shields the two stems of the pseudoknot, sitting in the major groove of the coaxial stack.Key words: ribosomes, translational control, r-protein S15, pseudoknot, RNA–protein recognition.
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48

Nejat, Naghmeh, Ganesan Vadamalai, Robert E. Davis, Nigel A. Harrison, Kamaruzaman Sijam, Matthew Dickinson, Siti Nor Akmar Abdullah, and Yan Zhao. "‘Candidatus Phytoplasma malaysianum’, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus)." International Journal of Systematic and Evolutionary Microbiology 63, Pt_2 (February 1, 2013): 540–48. http://dx.doi.org/10.1099/ijs.0.041467-0.

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This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described ‘ Candidatus Phytoplasma ’ species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described ‘ Ca. Phytoplasma ’ species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, ‘Candidatus Phytoplasma malaysianum’. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.
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49

Fewell, Sheara W., and John L. Woolford. "Ribosomal Protein S14 of Saccharomyces cerevisiae Regulates Its Expression by Binding toRPS14B Pre-mRNA and to 18S rRNA." Molecular and Cellular Biology 19, no. 1 (January 1, 1999): 826–34. http://dx.doi.org/10.1128/mcb.19.1.826.

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ABSTRACT Production of ribosomal protein S14 in Saccharomyces cerevisiae is coordinated with the rate of ribosome assembly by a feedback mechanism that represses expression of RPS14B. Three-hybrid assays in vivo and filter binding assays in vitro demonstrate that rpS14 directly binds to an RNA stem-loop structure inRPS14B pre-mRNA that is necessary for RPS14Bregulation. Moreover, rpS14 binds to a conserved helix in 18S rRNA with approximately five- to sixfold-greater affinity. These results support the model that RPS14B regulation is mediated by direct binding of rpS14 either to its pre-mRNA or to rRNA. Investigation of these interactions with the three-hybrid system reveals two regions of rpS14 that are involved in RNA recognition. D52G and E55G mutations in rpS14 alter the specificity of rpS14 for RNA, as indicated by increased affinity for RPS14B RNA but reduced affinity for the rRNA target. Deletion of the C terminus of rpS14, where multiple antibiotic resistance mutations map, prevents binding of rpS14 to RNA and production of functional 40S subunits. The emetine-resistant protein, rpS14-EmRR, which contains two mutations near the C terminus of rpS14, does not bind either RNA target in the three-hybrid or in vitro assays. This is the first direct demonstration that an antibiotic resistance mutation alters binding of an r protein to rRNA and is consistent with the hypothesis that antibiotic resistance mutations can result from local alterations in rRNA structure.
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50

Harrison, Nigel A., Robert E. Davis, Carlos Oropeza, Ericka E. Helmick, María Narváez, Simon Eden-Green, Michel Dollet, and Matthew Dickinson. "‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique." International Journal of Systematic and Evolutionary Microbiology 64, Pt_6 (June 1, 2014): 1890–99. http://dx.doi.org/10.1099/ijs.0.060053-0.

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In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus Phytoplasma ’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus Phytoplasma ’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.
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