scholarly journals 4.5S ribonucleic acid, a novel ribosome component in the chloroplasts of flowering plants

1979 ◽  
Vol 183 (3) ◽  
pp. 605-613 ◽  
Author(s):  
C M Bowman ◽  
T A Dyer
Keyword(s):  
Ribosomal Rna ◽  
Broad Bean ◽  
Large Subunit ◽  
Flowering Plants ◽  
5S Rrna ◽  
23S Rrna ◽  
Low Molecular Weight ◽  
5.8S Rrna ◽  
Wide Range ◽  
Predominant Variant

A species of low-molecular-weight ribosomal RNA, referred to as ‘4.5S rRNA’, was found in addition to 5S rRNA in the large subunit of chloroplast ribosomes of a wide range of flowering plants. It was shown by sequence analysis that several variants of this RNA may occur in a plant. Furthermore, although in most flowering plants the predominant variant contains about 100 nucleotides, in the broad bean it has less than 80. It seems, therefore, to be much more diverse in size and sequence than the other ribosomal RNA species. Like 5S rRNA, it does not contain modified nucleotides and it is also unusual in having an unphosphorylated 5′-end. It is apparently neither a homologue of cytosol 5.8S rRNA nor a fragment of 23S rRNA.

scholarly journals Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

2008 ◽  
Vol 28 (10) ◽  
pp. 3089-3100 ◽  
Author(s):  
Wayne A. Decatur ◽  
Murray N. Schnare
Keyword(s):  
Large Subunit ◽  
Consensus Sequence ◽  
5S Rrna ◽  
Stem Loop ◽  
Conserved Sequence ◽  
5.8S Rrna ◽  
Sequence Elements ◽  
The Individual ◽  
A Site ◽  
Large Subunit Rrna

ABSTRACT The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Ψs) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Ψ formation in 5S and 5.8S rRNA in which the unassigned Ψs occur. We show that while the formation of the Ψ in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Ψ in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Ψ in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.

Nature of the genome of the saprophytic spirochete Spirochaeta aurantia and its ribosomal RNA operons

2004 ◽  
Vol 50 (11) ◽  
pp. 967-971 ◽  
Author(s):  
Richard McLaughlin ◽  
David M Secko ◽  
Catherine J Paul ◽  
Andrew M Kropinski
Keyword(s):  
Ribosomal Rna ◽  
Gel Electrophoresis ◽  
Large Subunit ◽  
Complete Sequence ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pulsed Field ◽  
23S Rrna Gene ◽  
Intergenic Regions

Using restriction endonucleases DraI, AseI, and I-CeuI in conjunction with pulsed-field gel electrophoresis, we have shown that Spirochaeta aurantia M1 possesses a circular 3.98-Mb genome. This is the second largest spirochete chromosome yet analyzed. The observation that the latter enzyme cuts in 3 places suggests the presence of 3 copies of the large subunit (23S) rRNA gene (rrl), which was confirmed by Southern hybridizations. The complete sequence of 2 of the ribosomal RNA operons was determined, revealing that their structure resembled that of the typical member of the bacterial superkingdom: rrs (16S; 1561 bp), tRNA, rrl (23S; 2972 bp), and rrf (5S; 110 bp). The S. aurantia rrs–rrl intergenic regions, as with Treponema denticola, contain genes specifying a 73-nt tRNAAla (anticodon TGC) and a 77-nt tRNAIle (anticodon GAT).Key words: spirochete, pulsed-field gel electrophoresis, ribosomal RNA, operon, Spirochaeta aurantia.

scholarly journals Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation

2020 ◽  
Author(s):  
Radwa A. Hanafy ◽  
Britny Johnson ◽  
Noha H. Youssef ◽  
Mostafa S. Elshahed
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Subunit ◽  
Amplicon Sequencing ◽  
Sequencing Technology ◽  
Its1 Region ◽  
5.8S Rrna ◽  
Wide Range ◽  
Culture Independent ◽  
Long Read ◽  
Pacbio Smrt Sequencing

AbstractThe anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of ingested plant material. Accurate assessment of AGF diversity has been hampered by inherent deficiencies of the internal transcribed spacer1 (ITS1) region as a phylogenetic marker. Here, we report on the development and implementation of the D1/D2 region of the large ribosomal subunit (D1/D2 LSU) as a novel marker for assessing AGF diversity in culture-independent surveys. Sequencing a 1.4-1.5 Kbp amplicon encompassing the ITS1-5.8S rRNA-ITS2-D1/D2 LSU region in the ribosomal RNA locus from fungal strains and environmental samples generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior ITS1-based diversity surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing technology was conducted on fecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified in the 17.7 K sequences obtained, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to twelve different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, and the culturability of a wide range of AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.

scholarly journals Nuclear Argonaute Piwi Gene Mutation Affects rRNA by Inducing rRNA Fragment Accumulation, Antisense Expression, and Defective Processing in Drosophila Ovaries

2020 ◽  
Vol 21 (3) ◽  
pp. 1119
Author(s):  
Anastasia D. Stolyarenko
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Gene Mutation ◽  
Ribosomal Rna ◽  
5S Rrna ◽  
Rna Surveillance ◽  
5.8S Rrna ◽  
Argonaute Family ◽  
Main Component ◽  
Pirna Pathway

Drosophila key nuclear piRNA silencing pathway protein Piwi of the Argonaute family has been classically studied as a factor controlling transposable elements and fertility. Piwi has been shown to concentrate in the nucleolus for reasons largely unknown. Ribosomal RNA is the main component of the nucleolus. In this work the effect of a piwi mutation on rRNA is described. This work led to three important conclusions: A mutation in piwi induces antisense 5S rRNA expression, a processing defect of 2S rRNA orthologous to the 3′-end of eukaryotic 5.8S rRNA, and accumulation of fragments of all five rRNAs in Drosophila melanogaster ovaries. Hypotheses to explain these phenomena are proposed, possibly involving the interaction of the components of the piRNA pathway with the RNA surveillance machinery.

Variety of nonsense suppressor phenotypes associated with mutational changes at conserved sites in Escherichia coli ribosomal RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 925-931 ◽  
Author(s):  
Emanuel J. Murgola ◽  
Frances T. Pagel ◽  
Kathryn A. Hijazi ◽  
Alexey L. Arkov ◽  
Wenbing Xu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Ribosomal Rna ◽  
Intramolecular Interaction ◽  
Large Subunit ◽  
Chain Termination ◽  
Peptide Chain ◽  
Nonsense Suppression ◽  
23S Rrna ◽  
Nonsense Mutations

To screen for ribosomal RNA mutants defective in peptide chain termination, we have been looking for rRNA mutants that exhibit different patterns of suppression of nonsense mutations and that do not suppress missense mutations at the same positions in the same reporter gene. The rRNA mutations were induced by segment-directed randomly mutagenic PCR treatment of a cloned rrnB operon, followed by subcloning of the mutagenesis products and transformation of strains containing different nonsense mutations in the Escherichia coli trpA gene. To date, we have repeatedly obtained only two small sets of mutations, one in the 3′ domain of 16S rRNA, at five nucleotides out of the 610 mutagenized (two in helix 34 and three in helix 44), and the other in 23S rRNA at only four neighboring nucleotide positions (in a highly conserved hexanucleotide loop) within me 1.4 kb mutagenized segment. There is variety, however, in the suppression patterns of the mutants, ranging from suppression of UAG or UGA, through suppression of UAG and UGA, but not UAA, to suppression of all three termination codons. The two helices in 16S rRNA have previously been associated both physically and functionally with the decoding center of the ribosome. The 23S region is part of the binding site for the large subunit protein L11 and the antibiotic thiostrepton, both of which have been shown to affect peptide chain termination. Finally, we have demonstrated that the 23S mutant A1093, which suppresses trpA UGA mutations very efficiently, is lethal at temperatures above 36 °C (when highly expressed). This lethality is overcome by secondary 23S rRNA mutations in domain V. Our results suggest that specific regions of 16S and 23S rRNA are involved in peptide chain termination, that the lethality of A1093 is caused by high-level UGA suppression, and that intramolecular interaction between domains II and V of 23S rRNA may play a role in peptide chain termination at the UGA stop codon.Key words: 16S and 23S rRNAs, PCR mutagenesis, nonsense suppression, peptide chain termination, intramolecular interaction.

scholarly journals Cryo-Electron Microscopy Visualization of a Large Insertion in the 5S ribosomal RNA of the Extremely Halophilic Archaeon Halococcus morrhuae

2020 ◽  
Author(s):  
Madhan R Tirumalai ◽  
Jason T Kaelber ◽  
Donghyun R Park ◽  
Quyen Tran ◽  
George E Fox
Keyword(s):  
Electron Microscopy ◽  
Ribosomal Rna ◽  
Large Subunit ◽  
Insertion Site ◽  
5S Rrna ◽  
Extreme Halophile ◽  
Cryo Electron Microscopy ◽  
Junction Site ◽  
Nucleotide Insertion ◽  
Extremely Halophilic Archaeon

AbstractThe extreme halophile Halococcus morrhuae (ATCC® 17082) contains a 108-nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo-electron microscopy reconstruction of the native large subunit at subnanometer resolution. The insertion site forms a four-way junction that fully preserves the canonical 5S rRNA structure. Moving away from the junction site, the inserted region is conformationally flexible and does not pack tightly against the large subunit.

scholarly journals Nucleotide sequence analyses of the cytoplasmic 5S ribosomal ribonucleic acid from five species of flowering plants

1973 ◽  
Vol 135 (4) ◽  
pp. 845-851 ◽  
Author(s):  
P. I. Payne ◽  
M. J. Corry ◽  
T. A. Dyer
Keyword(s):  
Broad Bean ◽  
Flowering Plants ◽  
5S Rrna ◽  
Sequence Analyses ◽  
Two Dimensional Electrophoresis ◽  
Complementary Sequences ◽  
Ribosomal Ribonucleic Acid ◽  
Rrna Species ◽  
Dimensional Electrophoresis ◽  
Dwarf Bean

Broad-bean 5S rRNA labelled with32P was digested separately with T1 and pancreatic A ribonucleases and the resulting oligonucleotides (20 and 18 respectively) were fractionated by two-dimensional electrophoresis. The oligonucleotides were analysed further and 32 of them have been completely sequenced. They were compared with those of 5S rRNA from dwarf bean, sunflower, tomato and rye. Sequence differences were found at both the 3′- and 5′-termini and at up to nine other positions. Most base substitutions were transitions between C and U. In common with other 5S rRNA species that have been analysed the ends of the molecule in each plant species have complementary sequences.

scholarly journals Structure and functions of 5S rRNA.

2001 ◽  
Vol 48 (1) ◽  
pp. 191-198 ◽  
Author(s):  
M Z Barciszewska ◽  
M Szymański ◽  
V A Erdmann ◽  
J Barciszewski
Keyword(s):  
Messenger Rna ◽  
Protein Biosynthesis ◽  
Large Subunit ◽  
Genetic Material ◽  
Ribosomal Subunit ◽  
Peptide Bond ◽  
Small Subunit ◽  
5S Rrna ◽  
23S Rrna ◽  
Peptide Bond Formation

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all organisms. It is composed of two-subunit, ribonucleoprotein particles that translate the genetic material into an encoded polypeptides. The small subunit is the site of codon-anticodon interaction between the messenger RNA (mRNA) and transfer RNA (tRNA) substrates, and the large subunit catalyses peptide bond formation. The peptidyltransferase activity is fulfilled by 23S rRNA, which means that ribosome is a ribozyme. 5S rRNA is a conserved component of the large ribosomal subunit that is thought to enhance protein synthesis by stabilizing ribosome structure. This paper shortly summarises new results obtained on the structure and function of 5S rRNA.

scholarly journals Single enzyme RT-PCR of full-length ribosomal RNA

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Michael J Hammerling ◽  
Danielle J Yoesep ◽  
Michael C Jewett
Keyword(s):  
Ribosomal Rna ◽  
Reverse Transcription ◽  
Large Subunit ◽  
Small Subunit ◽  
23S Rrna ◽  
Rt Pcr ◽  
Reverse Transcriptases ◽  
Reverse Transcription Pcr ◽  
Translation Apparatus ◽  
Commercial Kits

Abstract The ribosome is a two-subunit, macromolecular machine composed of RNA and proteins that carries out the polymerization of α-amino acids into polypeptides. Efforts to engineer ribosomal RNA (rRNA) deepen our understanding of molecular translation and provide opportunities to expand the chemistry of life by creating ribosomes with altered properties. Toward these efforts, reverse transcription PCR (RT-PCR) of the entire 16S and 23S rRNAs, which make up the 30S small subunit and 50S large subunit, respectively, is important for isolating desired phenotypes. However, reverse transcription of rRNA is challenging due to extensive secondary structure and post-transcriptional modifications. One key challenge is that existing commercial kits for RT-PCR rely on reverse transcriptases that lack the extreme thermostability and processivity found in many commercial DNA polymerases, which can result in subpar performance on challenging templates. Here, we develop methods employing a synthetic thermostable reverse transcriptase (RTX) to enable and optimize RT-PCR of the complete Escherichia coli 16S and 23S rRNAs. We also characterize the error rate of RTX when traversing the various post-transcriptional modifications of the 23S rRNA. We anticipate that this work will facilitate efforts to study and characterize many naturally occurring long RNAs and to engineer the translation apparatus for synthetic biology.

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