1887

Chapter 29 : Modified Nucleosides Always Were: an Evolutionary Model

Authors: Nicolas Cermakian1, Robert Cedergren1
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Département de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
Content Type: Monograph
Publication Year: 1998

Category: Microbial Genetics and Molecular Biology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Modified Nucleosides Always Were: an Evolutionary Model, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap29-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap29-2.gif

Abstract:

This chapter evaluates the distribution of modified nucleosides in certain RNA species of the three domains of life (archaea, bacteria, and eukaryotes). Fourteen modifications are present in all three domains and of these several are found at comparable positions in tRNAs . First, most of the conserved modified nucleosides are in or near the anticodon loop. There is strong phylogenetic evidence for the early appearance of modified nucleosides. The incorporation of modified nucleosides into nucleic acid polymers is quite plausible, and the use of a particular nucleoside may depend only on its concentration in the primordial soup. Again, considering the chemistry of nucleosides, it would seem that the moderately modified nucleosides would be present in the highest concentrations in the primordial soup along with the standard nucleosides. In parallel, the phylogenetic evidence suggests that some simple modified nucleosides existed at the point when the major organismal groups diverged. In the case of tRNAs, there is no evidence for present-day RNA guiding, although such a system could be imagined early in the evolution of replicating cells. The current evidence of the enzymes involved in RNA-guided modification leaves the door open to speculation that RNA has a greater role in this process than simply guiding modification.

Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29

Key Concept Ranking

Small Nuclear RNA
0.46423987
Small Nucleolar RNA
0.46423987
Small Nuclear RNA
0.46423987
Small Nucleolar RNA
0.46423987
Small Nuclear RNA
0.46423987
Small Nucleolar RNA
0.46423987
Small Nuclear RNA
0.46423987
Small Nucleolar RNA
0.46423987
0.46423987
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Modified Nucleosides Always Were: an Evolutionary Model
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap29-1,webId=/content/author/10.1128/9781555818296.chap29-1,properties={foaf_givenname=Nicolas, foaf_name=Nicolas Cermakian, foaf_surname=Cermakian, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap29-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap29-2,webId=/content/author/10.1128/9781555818296.chap29-2,properties={foaf_givenname=Robert, foaf_name=Robert Cedergren, foaf_surname=Cedergren, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap29-aff1]]}]]
Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29
/content/10.1128/9781555818296.chap29.fig29-1
Figure 1

Nucleoside modifications likely to have been occurring in the cenancestor and in the RNA world. The upper part of the figure presents the results of the phylogenetic analysis of modified nucleotides. The data are from Table 1 and Appendix 1. The modified nucleosides found at corresponding positions in tRNAs from the three domains ( Table 1 ) are in bold. The modified nucleosides found in rRNAs of all three domains are underlined ( Table 2 ). Derived modifications are considered to have occurred later in evolution. The lower part of the figure refers to the discussion about the prebiotic world and RNA world. See the text for more details.

10.1128/9781555818296/fig29-1_thmb.gif
10.1128/9781555818296/fig29-1.gif
Image of Figure 1
Figure 1

Nucleoside modifications likely to have been occurring in the cenancestor and in the RNA world. The upper part of the figure presents the results of the phylogenetic analysis of modified nucleotides. The data are from Table 1 and Appendix 1. The modified nucleosides found at corresponding positions in tRNAs from the three domains ( Table 1 ) are in bold. The modified nucleosides found in rRNAs of all three domains are underlined ( Table 2 ). Derived modifications are considered to have occurred later in evolution. The lower part of the figure refers to the discussion about the prebiotic world and RNA world. See the text for more details.

Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818296.chap29
1. Björk, G. R., 1995. Biosynthesis and function of modified nucleosides, p. 165– 205. In D. Soil, and U. L. RajBhandary (ed.), tRNA: Structure, Biosynthesis, and Function. American Society for Microbiology, Washington, D.C.
2. Bussière, F.,, and J.-P. Perreault. 1995. On the road to a DNA-protein world. RNA 1: 451– 452.
3. Cedergren, R.,, and H. Grosjean. 1987. On the primacy of primordial RNA. BioSystems 20: 175– 180.
4. Cedergren, R.,, H. Grosjean,, and B. Larue. 1986. Primordial reading of genetic information. BioSystems 19: 259– 266.
5. Chartrand, P.,, S. C. Harvey,, G. Ferbeyre,, N. Usman,, and R. Cedergren. 1995. An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain. Nucleic Acids Res. 23: 4092– 4096.
6. Conrad, F.,, A. Hanne,, R. K. Gaur,, and G. Krupp. 1995. Enzymatic synthesis of 2'-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates. Nucleic Acids Res. 23: 1845– 1853.
7. Covello, P. S.,, and M. W. Gray. 1993. On the evolution of RNA editing. Trends Genet. 9: 265– 268.
8. Cuenoud, B.,, and J. W. Szostak. 1995. A DNA metalloenzyme with DNA ligase activity. Nature 375: 611– 614.
9. Darnell, J. E.,, and W. F. Doolittle. 1986. Speculations on the early course of evolution. Proc. Natl. Acad. Sci. USA 83: 1271– 1275.
10. Ferris, J. P.,, A. R. Hill,, R. Liu,, and L. E. Orgel. 1996. Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381: 59– 61.
11. Freyer, R.,, M. Kiefer-Meyer,, and H. Kössel. 1997. Occurence of plastid RNA editing in all major lineages of land plants. Proc. Natl. Acad. Sci. USA 94: 6285– 6290.
12. Gilbert, W. 1978. Why genes in pieces? Nature 271: 501.
13. Gilbert, W. 1986. The RNA world. Nature 319: 618.
14. Grosjean, H.,, F. Constantinesco,, D. Foiret,, and N. Benachenhou. 1995a. A novel enzymatic pathway leading to 1-methylinosine modification in Haloferax volcanii tRNA. Nucleic Acids Res. 23: 4312– 4319.
15. Grosjean, H.,, M. Sprinzl,, and S. Steinberg. 1995b. Posttranscrip-tionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77: 139– 141.
16. Grosjean, H.,, J. Edqvist,, K. B. Strâby,, and R. Giegé. 1996. Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J. Mol. Biol. 255: 67– 85.
17. Grosjean, H.,, Z. Szweykowska-Kulinska,, Y. Motorin,, F. Fasiolo,, and G. Simos. 1997. Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: a review. Biochimie 79: 293– 302.
18. Helm, M.,, H. Brulé,, F. Degoul,, C. Cepanec,, J. P. Leroux,, R. Giegé,, and C. Florentz. 1997. The presence of a modified nucleotide is required for the cloverleaf folding of a human mitochondrial tRNA. Oral presentation 3-13 of the 17th International tRNA Workshop, May 10-15, Kazusa Akademia Center, Chiba, Japan.
19. Herbert, A. 1996. RNA editing, introns and evolution. Trends Genet. 12: 6– 9.
20. Hurst, L. D.,, and G. T. McVean. 1996. A difficult phase for intron-early. Curr. Biol. 6: 533– 536.
21. Joyce, G. F.,, and L. E. Orgel,. 1993. Prospects for understanding the origin of the RNA world, p. 1– 25. In R. F. Gesteland, and J. F. Atkins (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
22. Kauffman, S. A. 1993. The Origins of Order. Self-Organization and Selection in Evolution. Oxford University Press, New York, N.Y.
23. Lane, B. G.,, J. Ofengand,, and M. W. Gray. 1995. Pseudouridine and 02'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77: 7– 15.
24. Lazcano, A., 1994a. The transition from nonliving to living, p. 61– 69. In S. Bengtson (ed.), Early Life on Earth. Columbia University Press, New York, N.Y.
25. Lazcano, A., 1994b. The RNA world, its predecessors, and its descendants, p. 70– 80. In S. Bengtson (ed.), Early Life on Earth. Columbia University Press, New York, N.Y.
26. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1994. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22: 2183– 2196.
27. Mazaki, H.,, T. Ogawa,, K. Tomita,, T. Ueda,, K. Watanabe,, and T. Uozumi. 1997. Colicin E5: a novel ribonuclease targeting a specific group of tRNAs. Oral presentation 2-1 of the 17th International tRNA Workshop, May 10-15, Kazusa Akademia Center, Chiba, Japan.
28. Ofengand, J.,, and A. Bakin. 1997. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebac-teria, mitochondria and chloroplasts. J. Mol. Biol. 266: 246– 268.
29. Osawa, S.,, T. H. Jukes,, K. Watanabe,, and A. Muto. 1992. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56: 229– 264.
30. Peracchi, A.,, L. Beigelman,, N. Usman,, and D. Herschlag. 1996. Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases. Proc. Natl. Acad. Sci. USA 93: 11522– 11527.
31. Perreault, J.-P.,, T. F. Wu,, B. Cousineau,, K. K. Ogilvie,, and R. Cedergren. 1990. Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity. Nature 344: 565– 567.
32. Scott, J. 1995. A place in the world for RNA editing. Cell 81: 833– 836.
33. Simpson, L. 1990. RNA editing—a novel genetic phenomenon? Science 250: 512– 513.
34. Szathmáry, E. 1997. The first two billion years. Nature 387: 662– 663.
35. Steinberg, S.,, and R. Cedergren. 1996. A correlation between N2-dimethylguanosine presence and alternate tRNA conformers. RNA 1: 886– 891.
36. Usman, N.,, L. Beigelman,, and J. A. McSwiggen. 1996. Hammerhead ribozyme engineering. Curr. Opin. Struct. Biol. 6: 527– 533.
37. Weiner, A. M.,, and N. Maizels. 1990. RNA editing: guided but not templated? Cell 61: 917– 920.
38. Yang, J. H.,, N. Usman,, P. Chartrand,, and R. Cedergren. 1992. Minimum ribonucleotide requirement for catalysis by the RNA hammerhead domain. Biochemistry 31: 5005– 5009.
39. Yu, W.,, and W. Schuster. 1995. Evidence for asite-specific cyti-dine deamination reaction involved in ? to U RNA editing of plant mitochondria. J. Biol. Chem. 270: 18227– 18233.

Tables

Modified Nucleosides Always Were: an Evolutionary Model
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap29-1,webId=/content/author/10.1128/9781555818296.chap29-1,properties={foaf_givenname=Nicolas, foaf_name=Nicolas Cermakian, foaf_surname=Cermakian, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap29-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818296.chap29-2,webId=/content/author/10.1128/9781555818296.chap29-2,properties={foaf_givenname=Robert, foaf_name=Robert Cedergren, foaf_surname=Cedergren, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818296.chap29-aff1]]}]]
Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29
/content/10.1128/9781555818296.chap29.tab29-1
Table 1

Modified nucleosides found at corresponding positions in tRNAs from eukaryotes, bacteria, and archaea

10.1128/9781555818296/tab29-1_thmb.gif
10.1128/9781555818296/tab29-1.gif
Generic image for table
Table 1

Modified nucleosides found at corresponding positions in tRNAs from eukaryotes, bacteria, and archaea

Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29
/content/10.1128/9781555818296.chap29.tab29-2
Table 2

Conserved modified nucleosides in rRNAs from eukaryotes, bacteria, and archaea

10.1128/9781555818296/tab29-2_thmb.gif
10.1128/9781555818296/tab29-2.gif
Generic image for table
Table 2

Conserved modified nucleosides in rRNAs from eukaryotes, bacteria, and archaea

Citation: Cermakian N, Cedergren R. 1998. Modified Nucleosides Always Were: an Evolutionary Model, p 535-541. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch29

Back to top
This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error