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Ribosomal DNA

January 01, 1970

Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. These sequences regulate transcription initiation and amplification, and contain both transcribed and non-transcribed spacer segments.

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.
Nucleolus with pre-rRNA components called Introns and Exons.

In the human genome there are 5 chromosomes with nucleolus organizer regions: the acrocentric chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5). The genes that are responsible for encoding the various sub-units of rRNA are located across multiple chromosomes in humans. But the genes that encode for rRNA are highly conserved across the domains, with only the copy numbers involved for the genes having varying numbers per species.[1] In Bacteria, Archaea, and chloroplasts the rRNA is composed of different (smaller) units, the large (23S) ribosomal RNA, 16S ribosomal RNA and 5S rRNA. The 16S rRNA is widely used for phylogenetic studies.[2]

Eukaryotes edit

The rRNA transcribed from the approximately 600 rDNA repeats forms the most abundant section of RNA found in cells of eukaryotes.[1] Ribosomes are assemblies of proteins and rRNA molecules that translate mRNA molecules to produce proteins. As shown in the figure, rDNA of eukaryotes consists of a tandem repeat of a unit segment, 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.[3] 5S rDNA is also present in independent tandem repeats as in Drosophila.[3] DNA regions that are repetitive often undergo recombination events. The rDNA repeats have many regulatory mechanisms that keep the DNA from undergoing mutations, thus keeping the rDNA conserved.[1]

In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA. The rRNA transcriptional units are clustered in tandem repeats. These rDNA regions are also called nucleolus organizer regions, as they give rise to the nucleolus. 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]

Sequence homogeneity edit

In the large rDNA array, polymorphisms between rDNA repeat units are very low, indicating that rDNA tandem arrays are evolving through concerted evolution.[3] However, the mechanism of concerted evolution is imperfect, such that polymorphisms between repeats within an individual can occur at significant levels and may confound phylogenetic analyses for closely related organisms.[4][5]

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.[6] They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion.[6]

Sequence divergence edit

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.[7] 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.[8] In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily.[9][10] 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.[11]

Recombination-stimulating activity edit

A fragment of yeast rDNA containing the 5S gene, non-transcribed spacer DNA, and part of the 35S gene has localized cis-acting mitotic recombination stimulating activity.[12] This DNA fragment contains a mitotic recombination hotspot, referred to as HOT1. HOT1 expresses recombination-stimulating activity when it is inserted into novel locations in the yeast genome. HOT1 includes an RNA polymerase I (PolI) transcription promoter that catalyzes 35S ribosomal 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 of recombination.[13]

Clinical significance edit

Diseases can be associated with DNA mutations where DNA can be expanded, such as Huntington'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 as Bloom 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.[14]

References edit

  1. ^ a b c d Warmerdam, Daniël O.; Wolthuis, Rob M. F. (2019-03-01). "Keeping ribosomal DNA intact: a repeating challenge". Chromosome Research. 27 (1): 57–72. doi:10.1007/s10577-018-9594-z. ISSN 1573-6849. PMC 6394564. PMID 30556094.
  2. ^ Weisburg WG, Barns SM, Pelletier DA, Lane DJ (January 1991). "16S ribosomal DNA amplification for phylogenetic study". Journal of Bacteriology. 173 (2): 697–703. doi:10.1128/jb.173.2.697-703.1991. PMC 207061. PMID 1987160.
  3. ^ a b c Richard GF, Kerrest A, Dujon B (December 2008). "Comparative genomics and molecular dynamics of DNA repeats in eukaryotes". Microbiology and Molecular Biology Reviews. 72 (4): 686–727. doi:10.1128/MMBR.00011-08. PMC 2593564. PMID 19052325.
  4. ^ Alvarez I, Wendel JF (December 2003). "Ribosomal ITS sequences and plant phylogenetic inference". Molecular Phylogenetics and Evolution. 29 (3): 417–34. doi:10.1016/S1055-7903(03)00208-2. PMID 14615184.
  5. ^ Weitemier K, Straub SC, Fishbein M, Liston A (2015). "Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)". PeerJ. 3: e718. doi:10.7717/peerj.718. PMC 4304868. PMID 25653903.
  6. ^ a b Päques F, Samson ML, Jordan P, Wegnez M (November 1995). "Structural evolution of the Drosophila 5S ribosomal genes". Journal of Molecular Evolution. 41 (5): 615–21. Bibcode:1995JMolE..41..615P. doi:10.1007/bf00175820. PMID 7490776. S2CID 6911205.
  7. ^ Sumida M, Kato Y, Kurabayashi A (April 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 & Genetic Systems. 79 (2): 105–18. doi:10.1266/ggs.79.105. PMID 15215676.
  8. ^ Nazar RN, Sitz TO, Busch H (February 1976). "Sequence homologies in mammalian 5.8S ribosomal RNA". Biochemistry. 15 (3): 505–8. doi:10.1021/bi00648a008. PMID 1252408.
  9. ^ Fengyi MY, Jiannong X, Zheming Z (1998). "Sequence differences of rDNA-ITS2 and species-diagnostic PCR assay of Anopheles sinensis and Anopheles anthropophagus from China" (PDF). J Med Coll PLA. 13: 123–128.
  10. ^ 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)" (PDF). Zootaxa. 939: 1–8. doi:10.11646/zootaxa.939.1.1. from the original on October 1, 2012.
  11. ^ Hillis DM, Dixon MT (December 1991). "Ribosomal DNA: molecular evolution and phylogenetic inference". The Quarterly Review of Biology. 66 (4): 411–53. doi:10.1086/417338. PMID 1784710. S2CID 32027097.
  12. ^ Keil RL, Roeder GS (December 1984). "Cis-acting, recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae". Cell. 39 (2 Pt 1): 377–86. doi:10.1016/0092-8674(84)90016-3. PMID 6094015.
  13. ^ Serizawa N, Horiuchi T, Kobayashi T (April 2004). "Transcription-mediated hyper-recombination in HOT1". Genes to Cells. 9 (4): 305–15. doi:10.1111/j.1356-9597.2004.00729.x. PMID 15066122. S2CID 23978914.
  14. ^ Warmerdam DO, Wolthuis RM (March 2019). "Keeping ribosomal DNA intact: a repeating challenge". Chromosome Research. 27 (1–2): 57–72. doi:10.1007/s10577-018-9594-z. PMC 6394564. PMID 30556094.

January 01, 1970
ribosomal, this, article, missing, information, about, bacteria, organelle, archaea, rdna, operons, ones, technically, polycistronic, canonical, inclusion, these, groups, plastid, occurrence, nonclassical, unlinked, variants, pmid, 31712737, please, expand, ar. This article is 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 the talk page October 2021 Ribosomal DNA rDNA is a DNA sequence that codes for ribosomal RNA These sequences regulate transcription initiation and amplification and contain both transcribed and non transcribed spacer segments 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 Nucleolus with pre rRNA components called Introns and Exons In the human genome there are 5 chromosomes with nucleolus organizer regions the acrocentric chromosomes 13 RNR1 14 RNR2 15 RNR3 21 RNR4 and 22 RNR5 The genes that are responsible for encoding the various sub units of rRNA are located across multiple chromosomes in humans But the genes that encode for rRNA are highly conserved across the domains with only the copy numbers involved for the genes having varying numbers per species 1 In Bacteria Archaea and chloroplasts the rRNA is composed of different smaller units the large 23S ribosomal RNA 16S ribosomal RNA and 5S rRNA The 16S rRNA is widely used for phylogenetic studies 2 Contents 1 Eukaryotes 2 Sequence homogeneity 3 Sequence divergence 4 Recombination stimulating activity 5 Clinical significance 6 ReferencesEukaryotes editThe rRNA transcribed from the approximately 600 rDNA repeats forms the most abundant section of RNA found in cells of eukaryotes 1 Ribosomes are assemblies of proteins and rRNA molecules that translate mRNA molecules to produce proteins As shown in the figure rDNA of eukaryotes consists of a tandem repeat of a unit segment 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 3 5S rDNA is also present in independent tandem repeats as in Drosophila 3 DNA regions that are repetitive often undergo recombination events The rDNA repeats have many regulatory mechanisms that keep the DNA from undergoing mutations thus keeping the rDNA conserved 1 In the nucleus the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA The rRNA transcriptional units are clustered in tandem repeats These rDNA regions are also called nucleolus organizer regions as they give rise to the nucleolus 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 Sequence homogeneity editIn the large rDNA array polymorphisms between rDNA repeat units are very low indicating that rDNA tandem arrays are evolving through concerted evolution 3 However the mechanism of concerted evolution is imperfect such that polymorphisms between repeats within an individual can occur at significant levels and may confound phylogenetic analyses for closely related organisms 4 5 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 6 They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion 6 Sequence divergence editThe 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 7 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 8 In cases for sibling species comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily 9 10 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 11 Recombination stimulating activity editA fragment of yeast rDNA containing the 5S gene non transcribed spacer DNA and part of the 35S gene has localized cis acting mitotic recombination stimulating activity 12 This DNA fragment contains a mitotic recombination hotspot referred to as HOT1 HOT1 expresses recombination stimulating activity when it is inserted into novel locations in the yeast genome HOT1 includes an RNA polymerase I PolI transcription promoter that catalyzes 35S ribosomal 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 of recombination 13 Clinical significance editDiseases can be associated with DNA mutations where DNA can be expanded such as Huntington 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 as Bloom 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 14 References edit a b c d Warmerdam Daniel O Wolthuis Rob M F 2019 03 01 Keeping ribosomal DNA intact a repeating challenge Chromosome Research 27 1 57 72 doi 10 1007 s10577 018 9594 z ISSN 1573 6849 PMC 6394564 PMID 30556094 Weisburg WG Barns SM Pelletier DA Lane DJ January 1991 16S ribosomal DNA amplification for phylogenetic study Journal of Bacteriology 173 2 697 703 doi 10 1128 jb 173 2 697 703 1991 PMC 207061 PMID 1987160 a b c Richard GF Kerrest A Dujon B December 2008 Comparative genomics and molecular dynamics of DNA repeats in eukaryotes Microbiology and Molecular Biology Reviews 72 4 686 727 doi 10 1128 MMBR 00011 08 PMC 2593564 PMID 19052325 Alvarez I Wendel JF December 2003 Ribosomal ITS sequences and plant phylogenetic inference Molecular Phylogenetics and Evolution 29 3 417 34 doi 10 1016 S1055 7903 03 00208 2 PMID 14615184 Weitemier K Straub SC Fishbein M Liston A 2015 Intragenomic polymorphisms among high copy loci a genus wide study of nuclear ribosomal DNA in Asclepias Apocynaceae PeerJ 3 e718 doi 10 7717 peerj 718 PMC 4304868 PMID 25653903 a b Paques F Samson ML Jordan P Wegnez M November 1995 Structural evolution of the Drosophila 5S ribosomal genes Journal of Molecular Evolution 41 5 615 21 Bibcode 1995JMolE 41 615P doi 10 1007 bf00175820 PMID 7490776 S2CID 6911205 Sumida M Kato Y Kurabayashi A April 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 amp Genetic Systems 79 2 105 18 doi 10 1266 ggs 79 105 PMID 15215676 Nazar RN Sitz TO Busch H February 1976 Sequence homologies in mammalian 5 8S ribosomal RNA Biochemistry 15 3 505 8 doi 10 1021 bi00648a008 PMID 1252408 Fengyi MY Jiannong X Zheming Z 1998 Sequence differences of rDNA ITS2 and species diagnostic PCR assay of Anopheles sinensis and Anopheles anthropophagus from China PDF J Med Coll PLA 13 123 128 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 PDF Zootaxa 939 1 8 doi 10 11646 zootaxa 939 1 1 Archived from the original on October 1 2012 Hillis DM Dixon MT December 1991 Ribosomal DNA molecular evolution and phylogenetic inference The Quarterly Review of Biology 66 4 411 53 doi 10 1086 417338 PMID 1784710 S2CID 32027097 Keil RL Roeder GS December 1984 Cis acting recombination stimulating activity in a fragment of the ribosomal DNA of S cerevisiae Cell 39 2 Pt 1 377 86 doi 10 1016 0092 8674 84 90016 3 PMID 6094015 Serizawa N Horiuchi T Kobayashi T April 2004 Transcription mediated hyper recombination in HOT1 Genes to Cells 9 4 305 15 doi 10 1111 j 1356 9597 2004 00729 x PMID 15066122 S2CID 23978914 Warmerdam DO Wolthuis RM March 2019 Keeping ribosomal DNA intact a repeating challenge Chromosome Research 27 1 2 57 72 doi 10 1007 s10577 018 9594 z PMC 6394564 PMID 30556094 Retrieved from https en wikipedia org w index php title Ribosomal DNA amp oldid 1210831579, wikipedia, wiki, book, books, library,

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