Homoiterons and expansion in ribosomal RNAs

Parker, Michael S.; Sallee, Floyd R.; Park, Edwards A.; Parker, Steven L.

doi:10.1016/j.fob.2015.10.005

Cited by 15 publications

(31 citation statements)

References 73 publications

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“…The entire fragment is situated at the very top of the central protuberance. The longer hairpin is homoiteron-rich, which is a feature often seen in the expansion segments of eukaryotic rRNAs (Parker et al 2015). Interestingly, similar motifs are present in several prokaryotic genomes other than thermoanaerobacterial.…”

Section: Peptococcaceaementioning

confidence: 77%

Expansion Segments in Bacterial and Archaeal 5S Ribosomal RNAs

Степанов

Fox

2020

Preprint

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The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales. When several copies of 5S rRNA gene are present in a genome, the expanded versions may co-exist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.

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Section: Peptococcaceaementioning

confidence: 77%

Expansion Segments in Bacterial and Archaeal 5S Ribosomal RNAs

Степанов

Fox

2020

Preprint

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“…This study utilized the numbering of rRNA expansion segments described by Gerbi ( 1996 ) and Yokoyama and Suzuki ( 2008 ). The segment boundaries were derived from Chandramouli et al ( 2008 ) and Wakeman and Maden ( 1989 ) (see Parker et al, 2015 ) and are listed in Table S2 . The segment boundaries of human rRNAs were searched for in clustalW ( http://www.expasy.org ) alignments with other ribosomal RNAs to score the matching starting and ending nucleotides.…”

Section: Methodsmentioning

confidence: 99%

“…Compared to prokaryote 23S rRNAs, the large LSU rRNAs in eukaryotes show enlargement of up to 2,400 nucleotides (or up to 80% additional sequence), with a remarkable phylogenetically linked increase in both size and nucleotide bias from yeast to man (Chandramouli et al, 2008 ; Ben-Shem et al, 2010 ; Parker et al, 2015 ). This increase is linked to expansion segments added at strongly conserved insertion points, which enables use of the most expanded LSU RNA, human 28S rRNA, as a template for marking the expansion segment boundaries in 25-28S rRNAs across eukarya (Parker et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…In human 28S rRNA there are eight ESL of more than 50 nucleotides (nt), and two ESL of more than 700 nt, compared with four >50-nt expansion segments in 18S rRNA (abbreviated ESS; none larger than 180 nt) (Wakeman and Maden, 1989 ; Chandramouli et al, 2008 ). The large ESL are substantially exposed at the ribosome surface (Wakeman and Maden, 1989 ; Larsson and Nygård, 2001 ; Nygård et al, 2006 ; Chandramouli et al, 2008 ; Armache et al, 2010 ; Klinge et al, 2011 ), feature tracts that are not stably associated with ribosomal proteins (Larsson and Nygård, 2001 ; Chandramouli et al, 2008 ), and could be available for association with mRNAs as well as with non-ribosomal proteins and intracellular matrices (Parker et al, 2014 , 2015 ). The ESS appear to have no firm general pattern and could differ much in subdivisions across species (Chandramouli et al, 2008 ; Ben-Shem et al, 2011 ; Parker et al, 2015 ; Quade et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…An interaction of the 60S subunit with mRNA is only rarely assumed (Sloma and Nygård, 2001 ) although ESL are known to interact with extraribosomal entities (Leidig et al, 2013 ). The extremely GC-rich ES of vertebrate 28S rRNA (Clark et al, 1984 ; Wakeman and Maden, 1989 ; Chandramouli et al, 2008 ), which also are rich in G and C repeats (homoiterons; see Parker et al, 2015 ), may have roles in mobilization of mRNAs from mRNPs, by analogy e.g., with mRNP protein binding by polyriboguanylate (Barrieux and Rosenfeld, 1977 ); rRNA guanine is important in codon association with either 16S rRNA of prokaryotes or 18S rRNA of eukaryotes (Demeshkina et al, 2000 ) and G-rich rRNA motifs could generally complement mRNAs (Barendt et al, 2013 ). The mRNA sequences used in initial positioning on the ribosome (IRES sites) could interact with RNAs of either subunit.…”

Section: Introductionmentioning

confidence: 99%

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The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

et al. 2018

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Eukaryote ribosomal RNAs (rRNAs) have expanded in the course of phylogeny by addition of nucleotides in specific insertion areas, the expansion segments. These number about 40 in the larger (25–28S) rRNA (up to 2,400 nucleotides), and about 12 in the smaller (18S) rRNA (<700 nucleotides). Expansion of the larger rRNA shows a clear phylogenetic increase, with a dramatic rise in mammals and especially in hominids. Substantial portions of expansion segments in this RNA are not bound to ribosomal proteins, and may engage extraneous interactants, including messenger RNAs (mRNAs). Studies on the ribosome-mRNA interaction have focused on proteins of the smaller ribosomal subunit, with some examination of 18S rRNA. However, the expansion segments of human 28S rRNA show much higher density and numbers of mRNA matches than those of 18S rRNA, and also a higher density and match numbers than its own core parts. We have studied that with frequent and potentially stable matches containing 7–15 nucleotides. The expansion segments of 28S rRNA average more than 50 matches per mRNA even assuming only 5% of their sequence as available for such interaction. Large expansion segments 7, 15, and 27 of 28S rRNA also have copious long (≥10-nucleotide) matches to most human mRNAs, with frequencies much higher than in other 28S rRNA parts. Expansion segments 7 and 27 and especially segment 15 of 28S rRNA show large size increase in mammals compared to other metazoans, which could reflect a gain of function related to interaction with non-ribosomal partners. The 28S rRNA expansion segment 15 shows very high increments in size, guanosine, and cytidine nucleotide content and mRNA matching in mammals, and especially in hominids. With these segments (but not with other 28S rRNA or any 18S rRNA expansion segments) the density and number of matches are much higher in 5′-terminal than in 3′-terminal untranslated mRNA regions, which may relate to mRNA mobilization via 5′ termini. Matches in the expansion segments 7, 15, and 27 of human 28S rRNA appear as candidates for general interaction with mRNAs, especially those associated with intracellular matrices such as the endoplasmic reticulum.

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The story of rRNA expansion segments: Finding functionality amidst diversity

2022

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Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs.Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine-tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species-specific regulatory hub of protein synthesis.In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future.

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Homoiterons and expansion in ribosomal RNAs

Cited by 15 publications

References 73 publications

Expansion Segments in Bacterial and Archaeal 5S Ribosomal RNAs

Expansion Segments in Bacterial and Archaeal 5S Ribosomal RNAs

The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

The story of rRNA expansion segments: Finding functionality amidst diversity

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