Ribosomal DNA

The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S tracts and forms a tandem repetitive cluster; the 5S rDNA is coded separately. NTS, nontranscribed spacer, ETS, external transcribed spacer, ITS, internal transcribed spacers 1 and 2, numbered from 5' end.

Ribosomal DNA (rDNA) codes for ribosomal RNA. The ribosome is an intracellular macromolecule that produces proteins or polypeptide chains. The ribosome itself consists of a composite of proteins and RNA. As shown in the figure, rDNA consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes.^[1] 5S rDNA is also present in tandem repeats as in Drosophila.^[1] In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA. These rDNA regions are also called nucleolus organizer regions, as they give rise to the nucleolus. In the human genome there are 5 chromosomes with nucleolus organizer regions: chromosomes 13,14,15,21 and 22.

Sequence homogeneity of the repeat unit

In the large rDNA array, polymorphisms between rDNA repeat units are very low, indicating that rDNA tandem arrays are evolving through concerted evolution.^[1] 5S tandem repeat sequences in several Drosophila were compared with each other; the result revealed that insertions and deletions occurred frequently between species and often flanked by conserved sequences.^[2] They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion.^[2]

Sequence divergence to clarify phylogeny

The rDNA transcription tracts have low rate of polymorphism 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.^[3] 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.^[4] In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily.^[5][6] 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.^[7]

Notes

1. ^ ^{a b c} Richard GF, Kerrest A, Dujon B (2008). "Comparative genomics and molecular dynamics of DNA repeats in eukaryotes." Microbiol Mol Biol Rev 72(4): 686-727, PMID 19052325, Full text at PMC: 2593564, doi:10.1128/MMBR.00011-08.
2. ^ ^{a b} Pâques F, Samson ML, Jordan P, Wegnez M (1995). "Structural evolution of the Drosophila 5S ribosomal genes." J Mol Evol 41(5): 615-621, PMID 7490776.
3. ^ Sumida M, Kato Y, Kurabayashi A (2004). "Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata." Genes Genet Syst 79(2): 105-118, PMID 15215676.
4. ^ Nazar RN, Sitz TO, Busch H (1976). "Sequence homologies in mammalian 5.8S ribosomal RNA." Biochemistry 15(3): 505-508, PMID 1252408.
5. ^ Ma YJ, Qu FY, Xu JJ. (1998). "Sequence differences of rDNA-ITS2 and species-diagnostic PCR assay of Anopheles sinensis and Anopheles anthropophagus from China. J Med Coll PLA 13: 123-128. [1].
6. ^ Li C, Lee JS, Groebner JL, Kim HC, Klein TA, O'Guinn ML, Wilkerson RC (2005). "A newly recognized species in the Anopheles hyrcanus group and molecular identification of related species from the Republic of South Korea (Diptera: Culicidae)." Zootaxa 939: 1-8. [2].
7. ^ Hillis DM, Dixon MT (1991). "Ribosomal DNA: molecular evolution and phylogenetic inference." Quart Rev Biol 66(4): 411-453, PMID 1784710.