 | This articleis missing information about bacteria/organelle, archaea (rDNA operons — the euk ones are technically polycistronic too); canonical inclusion of 5S in these groups; plastid 4.5S; occurrence of nonclassical "unlinked" variants (PMID 31712737). Please expand the article to include this information. Further details may exist on thetalk page.(October 2021) |
Theribosomal DNA (abbreviatedrDNA) consists of a group ofribosomal RNA encoding genes and related regulatory elements, and is widespread in similar configuration in alldomains of life. The ribosomal DNA encodes the non-codingribosomal RNA, integral structural elements in the assembly ofribosomes, its importance making it the most abundant section of RNA found in cells ofeukaryotes.[1] Additionally, these segments includesregulatory sections, such as apromotor specific to theRNA polymerase I, as well as both transcribed and non-transcribedspacer segments.
Due to their high importance in the assembly ofribosomes forprotein biosynthesis, the rDNA genes are generally highly conserved inmolecular evolution. The number of copies can vary considerably per species.[1] Ribosomal DNA is widely used forphylogenetic studies.[2][3]
| Type | SSU rRNA | LSU rRNA |
|---|---|---|
| Eukaryotes | 18S rRNA | 28S rRNA 5.8S rRNA 5S rRNA |
| Bacteria | 16S rRNA | 23S rRNA 5S rRNA |
| Mitochondrial | MT-RNR1 (12S rRNA) | MT-RNR2 (16S rRNA) |
| Plastid | 16S rRNA | 23S rRNA 4.5S rRNA 5S rRNA |
The ribosomal DNA includes all genes coding for the non-coding structuralribosomal RNA molecules. Across alldomains of life, these are the structural sequences of thesmall subunit (16S or18S rRNA) and thelarge subunit (23S or28S rRNA). The assembly of the latter also include the5S rRNA as well as the additional5.8S rRNA in eukaryotes.
The rDNA-genes are commonly present with multiple copies in the genome, where they are organized in linked groups in most species, separated by aninternal transcribed spacer (ITS) and preceded by theExternal transcribed spacer (ETS). The5S rRNA is also linked to these rDNA region inprokaryotes, while it is located in separate repeating regions in mosteukaryotes.[4] They are transcribed together to a precursor RNA which is then processed to equal amounts of each rRNA.
The primary structural rRNA molecules inBacteria andArchaea are smaller than their counterparts in eukaryotes, grouped as16S rRNA and23S rRNA. Meanwhile, the5S rRNA also present in prokaryotes, is of a similar size to eukaryotes.
A notable amount of bacteria and archaea diverge from the canonical structure of the operon containing the rDNA genes, carrying the "unlinked" genes in different places of their genome.[5]
Ribosomal DNA inchloroplasts follows the structure of prokaryotic ribosomal DNA.
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The rDNA gene cluster of eukaryotes consists of the genes for the18S,5.8S and28S rRNA, separated by the twoITS-1 and ITS-2 spacers. The active genome of eukaryotes contains several hundred copies of the rDNA transcriptional unit astandem repeats, they are organized innucleolus organizer regions (NORs),[4] which in turn can be present at multipleloci in the genome.[6]
Similar to the structure of prokaryotes, the5S rRNA is appended to the rDNA cluster in theSaccharomycetes (Hemiascomycetes)[6] such asSaccharomyces cerevisiae.[4] Most eukaryotes however, carry the gene for the5S rRNA in separate gene repeats at different loci in the genome.[6][4]
5S rDNA is also present in independent tandem repeats as inDrosophila.[6] As repetitive DNA regions often undergo recombination events, the rDNA repeats have many regulatory mechanisms that keep the DNA from undergoing mutations,[example needed] thus keeping the rDNA conserved.[1]
In the nucleus, thenucleolus organizer regions give rise to thenucleolus, where the rDNA regions of the chromosome forms expanded chromosomal loops, accessible for transcription ofrRNA. In rDNA, the tandem repeats are mostly found in the nucleolus; but heterochromatic rDNA is found outside of the nucleolus. However, transcriptionally active rDNA resides inside of the nucleolus itself.[1]
Thehuman genome contains a total of 560 copies[4] of the rDNA transcriptional unit, spread across five chromosomes withnucleolus organizer regions. The repeat clusters are located on theacrocentric chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5).[7]
Inciliates, the presence of a generativemicronucleus next to the vegetativemacronucleus allows for the reduction of rDNA genes in the germline. The exact number of copies in the micronucleus core genome ranging from several copies inParamecium[8] as low as a single copy inTetrahymena thermophila[4] and otherTetrahymena species. Duringmacronucleus formation, the regions containing the rDNA gene clusters are amplified, dramatically increasing the amount of available templates for transcription up to several thousand copies. In some ciliate genera, such asTetrahymena or theHypotrich genusOxytricha,[8] extensive fragmentation of the amplified DNA leads to the formation of microchromosomes, centered on the rDNA transcriptional unit.[8] Similar processes are reported fromGlaucoma chattoni and to lesser extent fromParamecium.[8]
In the large rDNA array, polymorphisms between rDNA repeat units are very low, indicating that rDNA tandem arrays are evolving throughconcerted evolution.[6] However, the mechanism of concerted evolution is imperfect, such that polymorphisms between repeats within an individual can occur at significant levels and may confoundphylogenetic analyses for closely related organisms.[9][10]
5S tandem repeat sequences in severalDrosophila were compared with each other; the result revealed thatinsertions anddeletions occurred frequently between species and often flanked by conserved sequences.[11] They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion.[11]
The rDNA transcription tracts have low rate ofpolymorphism among species, which allows interspecific comparison to elucidate phylogenetic relationship using only a few specimens. Coding regions of rDNA are highly conserved among species but ITS regions are variable due to insertions, deletions, and point mutations. Between remote species as human and frog comparison of sequences at ITS tracts is not appropriate.[12] Conserved sequences at coding regions of rDNA allow comparisons of remote species, even between yeast and human. Human 5.8S rRNA has 75% identity with yeast 5.8S rRNA.[13]In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily.[14][15]The different coding regions of the rDNA repeats usually show distinct evolutionary rates. As a result, this DNA can provide phylogenetic information of species belonging to wide systematic levels.[2]
A fragment of yeast rDNA containing the 5S gene, non-transcribed spacer DNA, and part of the 35S gene has localized cis-actingmitotic recombination stimulating activity.[16] This DNA fragment contains a mitoticrecombination hotspot, referred to as HOT1. HOT1 expresses recombination-stimulating activity when it is inserted into novel locations in the yeastgenome. HOT1 includes anRNA polymerase I (PolI) transcriptionpromoter that catalyzes 35Sribosomal rRNA gene transcription. In a PolI defective mutant, the HOT1 hotspot recombination-stimulating activity is abolished. The level of PolI transcription in HOT1 appears to determine the level ofrecombination.[17]
Diseases can be associated with DNA mutations where DNA can be expanded, such asHuntington's disease, or lost due to deletion mutations. The same is true for mutations that occur in rDNA repeats; it has been found that if the genes that are associated with the synthesis of ribosomes are disrupted or mutated, it can result in various diseases associated with the skeleton or bone marrow. Also, any damage or disruption to the enzymes that protect the tandem repeats of the rDNA, can result in lower synthesis of ribosomes, which also lead to other defects in the cell. Neurological diseases can also arise from mutations in the rDNA tandem repeats, such asBloom syndrome, which occurs when the number of tandem repeats increases close to a hundred-fold; compared with that of the normal number of tandem repeats. Various types of cancers can also be born from mutations of the tandem repeats in the ribosomal DNA. Cell lines can become malignant from either a rearrangement of the tandem repeats, or an expansion of the repeats in the rDNA.[18]