Homoiterons and expansion in ribosomal RNAs
Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large R...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2015-01-01
|
| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1016/j.fob.2015.10.005 |
| _version_ | 1811206002792464384 |
|---|---|
| author | Michael S. Parker Floyd R. Sallee Edwards A. Park Steven L. Parker |
| author_facet | Michael S. Parker Floyd R. Sallee Edwards A. Park Steven L. Parker |
| author_sort | Michael S. Parker |
| collection | DOAJ |
| description | Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron‐rich double‐stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks. |
| first_indexed | 2024-04-12T03:41:11Z |
| format | Article |
| id | doaj.art-932a75ff5988473d97c98f1cbe24fdda |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-04-12T03:41:11Z |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-932a75ff5988473d97c98f1cbe24fdda2022-12-22T03:49:17ZengWileyFEBS Open Bio2211-54632015-01-015186487610.1016/j.fob.2015.10.005Homoiterons and expansion in ribosomal RNAsMichael S. Parker0Floyd R. Sallee1Edwards A. Park2Steven L. Parker3Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN 38152, USADepartment of Psychiatry, University of Cincinnati School of Medicine, Cincinnati, OH 45276, USADepartment of Pharmacology, University of Tennessee Health Sciences Center, Memphis, TN 38163, USADepartment of Pharmacology, University of Tennessee Health Sciences Center, Memphis, TN 38163, USARibosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron‐rich double‐stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks.https://doi.org/10.1016/j.fob.2015.10.005RNA expansion segmentRNA nucleotide biasRNA nucleotide repeat |
| spellingShingle | Michael S. Parker Floyd R. Sallee Edwards A. Park Steven L. Parker Homoiterons and expansion in ribosomal RNAs FEBS Open Bio RNA expansion segment RNA nucleotide bias RNA nucleotide repeat |
| title | Homoiterons and expansion in ribosomal RNAs |
| title_full | Homoiterons and expansion in ribosomal RNAs |
| title_fullStr | Homoiterons and expansion in ribosomal RNAs |
| title_full_unstemmed | Homoiterons and expansion in ribosomal RNAs |
| title_short | Homoiterons and expansion in ribosomal RNAs |
| title_sort | homoiterons and expansion in ribosomal rnas |
| topic | RNA expansion segment RNA nucleotide bias RNA nucleotide repeat |
| url | https://doi.org/10.1016/j.fob.2015.10.005 |
| work_keys_str_mv | AT michaelsparker homoiteronsandexpansioninribosomalrnas AT floydrsallee homoiteronsandexpansioninribosomalrnas AT edwardsapark homoiteronsandexpansioninribosomalrnas AT stevenlparker homoiteronsandexpansioninribosomalrnas |