The Wikipedia page for rDNA says "Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA" Also, the figure next to it says "The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S tracts and forms a tandem repetitive cluster". So, it gave me the impression that rDNA codes for both rRNA and the structural proteins of ribosome. Is that right?

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    $\begingroup$ Wrong. Read about ribosomal protein genes. $\endgroup$ – David Feb 23 '20 at 20:11
  • $\begingroup$ Thanks David! Could you tell me, what exactly is meant by "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." in the picture (en.wikipedia.org/wiki/Ribosomal_DNA#/media/…) $\endgroup$ – Noob Feb 23 '20 at 22:33

As well as messenger RNA (mRNA) that encodes protein, there are a variety of RNAs that have structural or regulatory roles and do not code for protein. Ribosomal RNAs (rRNA) are one such structural RNA. Like mRNA, rRNA (and other stable RNAs) are specified by genes in the chromosomal DNA, although the details of their transcription (the RNA polymerase employed and the nature of the promotors) may vary.

The mature eukaryotic ribosome contains three species of rRNA that are analogous to those in prokaryotes — 18S (cf. 16S), 28S (cf. 23S) and 5S (sizes for mammals). However there is an additional 5.8S species in eukaryotes. The questions addressed in the article are: 1. What genes and what transcripts give rise to these mature RNA species? and 2. Is there a single gene for each species or multiple repeated genes? A third, implicit, question is whether the situation in eukaryotes is similar to that in eukaryotes.

The answer to question 2 is given in the phrase “forms a tandem repetitive cluster” — there are multiple copies of the genes for 18S, 28S and 5.8S rRNA, clustered together one after another. These genes are separated (‘spaced apart’) by regions of the genome that are not transcribed, and are termed non-transcribed spacers (NTS).

(There are also multiple copies of the 5S rRNA gene, although these are only clustered in some species.)

The answer to the first question is that the 18S, 28S and 5.8S rRNA are transcribed from a single gene and are initially present in a single transcript. This is processed by ribonucleases to generate the three mature species. If one compares the sequences of the mature species with that of the gene/transcript one can identify portions of the initial rRNA transcript that are not present in any of the three mature species. These are termed transcribed spacers. The one at the 5′ end of the transcript is termed the external transcribed spacer (ETS), and those that are between the three mature species are termed internal transcribed spacer (ITS).

rDNA cluster in eukaryotes

The situation in prokaryotes differs from eukaryotes in so far as the 5S rRNA gene is part of the gene/transcript containing the 16S and 23S rRNAs, lying at the 3′ end of this. This is mentioned in the Wikipedia entry for Ribosomal RNA, rather than that for ribosomal DNA, quoted in the question, and illustrated in the figure below taken from the teaching web pages of Ross Hardison at Penn State University. Notice the transfer RNA gene in the transcript between the portions resulting in the mature 16S and 23S rRNAs.

enter image description here

  • $\begingroup$ Thank Dav! You have been very helpful to me. Thank you so much! $\endgroup$ – Noob Feb 24 '20 at 16:23
  • $\begingroup$ "rRNA are synthesized in a different pathway. In the nucleolus, the rRNAs combine with ribosomal proteins to form the large and small subunits of the ribosome. Ribosomal proteins are synthesized in the cytoplasm and transported to the nucleus for subassembly in the nucleolus. They autoassemble in a long complicated maturation process which ends in the cytoplasm (ER)". nature.com/articles/35030006 says there's more rRNA than protein in the ribosome, so there are a lot of copies of those few transcripts. Did they succeed in producing ribosomes in-vitro from the separated ingredients? $\endgroup$ – reuns Feb 28 '20 at 6:34
  • $\begingroup$ @reuns — As I understand it you are asking either one or two supplementary questions. In answer to the question in your final sentence. Nomura reconstituted bacterial ribosomes in 1968 (if I remember rightly) and showed that resistance (or sensitivity — I forget) to streptomycin was a property of one specific protein (S12). People I knew were trying unsuccessfully to do the same thing for eukaryotes in the early 70s, but I imagine (and seem to remember) that was subsequently achieved. As assembly in vivo occurs on the rRNA precursors, the reassembly in vitro is somewhat artificial. $\endgroup$ – David Feb 28 '20 at 8:46
  • $\begingroup$ Tks, also I realize what I said was wrong (for prokaryote) the 30s subunit contains only one single stranded rRNA (secondary structures make it locally double stranded) of 1500 nucleotides each containing about 20 non-hydrogen atoms gives the 30000 rRNA atoms mentioned in the nature article. Thus (for the small subunit) it is about assembling 1 rRNA and 21 proteins which is doable and has been achieved since 40 years. This explains why the map of the 30s is described in term of 5' central and 3' parts $\endgroup$ – reuns Feb 29 '20 at 4:04

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