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Polyadenylation

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Eukaryotic mature mRNA structure

Polyadenylation is the synthesis of a poly(A) tail, a stretch of RNA where all the bases are adenines, at the end of an RNA molecule. Polyadenylation is part of the route by which eukaryotes produce mature messenger RNA (mRNA) for translation, in the larger process of protein synthesis to produce proteins. At the end transcription, the last (3'-most) bit of the newly made RNA is cleaved off by a complex of proteins; this complex then synthesises the poly(A) tail at the RNA's 3' end. Polyadenylation can result in more than one RNA variant of a gene (similar to alternative splicing), depending on which polyadenylation site is used for the gene in a particular cell. The poly(A) tail is important for the stability of mRNA, and when the tail is shortened the mRNA is soon enzymatically degraded. For prokaryotic RNAs and some eukaryotic RNAs, polyadenylation instead promotes degradation.

Background

File:RNA chemical structure adenine.GIF
Chemical structure of RNA
Main article: RNA

The name poly(A) tail comes from the way RNA nucleotides are abbreviated, with a letter for the base the nucleotide contains (A for adenine, C for cytosine, G for guanine and U for uracil). RNA sequences are written in a 5' to 3' direction, where the 5' end is the part of the RNA molecule that is transcribed first, and the 3' end is the last transcribed part (transcription is the synthesis of RNA from a DNA template). The 3' end is also where the poly(A) tail is found, if it is a polyadenylated RNA.

Messenger RNA (mRNA) has a coding region that acts as a template for protein synthesis (translation). The rest of the mRNA, the untranslated regions, instead tune how active the mRNA is. The are also many RNAs that are not translated, called non-coding RNAs. Like the untranslated regions, many of these non-coding RNAs have regulatory roles.

Function

The poly(A) tail protects the mRNA molecule from degradation by exonucleases in the cytoplasm and aids in transcription termination, export of the mRNA from the nucleus, and translation. Almost all eukaryotic mRNAs are polyadenylated.[1][2] Many bacterial mRNAs are also polyadenylated, but here the poly(A) tail promotes degradation by the degradosome.[3]

For many non-coding RNAs, including tRNA, rRNA and snRNA, polyadenylation is a way of marking the RNA for degradation by the exosome in eukaryotes and archaea and degradosome in bacteria.[4][5] This targets misfolded RNAs in particular.[6] However, many eukaryotic non-coding RNAs are always polyadenylated at the end of transcription. For some of these, the poly(A) tail is not seen in the mature RNA as the ends are removed during processing (e.g. microRNAs), while for others the poly(A) tail is part of the final RNA (e.g. Xist).[7][8]

Mechanism

Proteins involved:[1]

CPSF: cleavage/polyadenylation specificity factor
CstF: cleavage stimulation factor
PAP: polyadenylate polymerase
PAB2: polyadenylate binding protein
CFI: cleavage facor I
CFII: cleavage factor II

The polyadenylation machinery in the nucleus of eukaryotes works on products of RNA polymerase II, such as precursor mRNA. Here, a multi-protein complex (see components on the right) promotes cleavage of the RNA 15–30 nucleotides downstream of a site which is recognised by CPSF.[9] This site is often the sequence AAUAAA on the RNA, but variants of it exist that bind more weakly to CPSF.[10] CstF binds to a GU-rich region further downstream.[11] A third site on the RNA (a set of UGUAA sequences in mammals), is recognised by CFI, which can recruit CPSF even if the AAUAAA sequence is missing.[12][13] The RNA is cleaved right after transcription, as CstF also binds to RNA polymerase II.[14] When the RNA is cleaved, polyadenylation starts, catalysed by polyadenylate polymerase. The reaction is RNA + n MgATP → RNA–(A)n + n MgPPi.[15] PAB2 increases the affinity of polyadenylate polymerase for the RNA for the first approximately 250 nucleotides, thus determing the length of the poly(A) tail.[16] CPSF is in contact with RNA polymerase II, which it promotes to terminate transcription.[17] The polyadenylation machinery is also linked by CFI to the spliceosome, a complex that removes introns from RNAs.[13] The role of CFII is unknown, but it is needed for cleavage.[18]

The polyadenylation of aberrant non-coding RNAs involves a different set of proteins. In eukaryotes, this is done by the TRAMP complex, which adds an around 40 nucleotides long tail to the 3' end.[19] Similarly, bacterial poly(A) tails, synthesised mainly by polyadenylate polymerase I, are 10–40 nucleotides long.[20]

Alternative polyadenylation

Results of using different polyadenylation sites on the same gene

Roughly half of all protein-coding genes have more than one polyadenylation site, so a gene can code for several mRNAs that differ in their 3' end.[21] For some genes there are several polyadenylation sites on the last exon, and for some genes they are spread over several exons.[22] The vast majority of poly(A) sites are found in the 3' untranslated regions, but some sites are found in introns, coding sequences and 5' untranslated regions.[23] Since alternative polyadenylation changes the length of the 3' untranslated region, it can change which binding sites for microRNAs the 3' untranslated region contains.[9] MicroRNAs repress translation and promote degradation of the mRNAs they bind to.[24]

The selection of which poly(A) site is used depends on the expression of the proteins that take part in polyadenylation. For example, the expression of CstF-64, a subunit of CstF, increases in macrophages in response to lipopolysaccharides (a group of bacterial compounds that trigger an immune response), resulting in the selection of weak poly(A) sites and thus shorter transcripts. This removes regulatory elements in the 3' untranslated regions of mRNAs for defense-related products like lysozyme and TNF-α, increasing the half-lives of these mRNAs.[25]

Deadenylation

After export to the cytoplasm, the poly(A) tail of most mRNAs gradually gets shorter in eukaryotic somatic cells, and mRNAs with shorter poly(A) tail are translated less and degraded sooner.[26] Deadenylation can be accelerated by microRNAs complementary to the 3' untranslated region of an mRNA, this deadenylation initiates degradation of the mRNA.[27] In the immature egg cells, mRNAs with shortened poly(A) tails are not degraded, but are stored without being translated. They are then activated by cytoplasmic polyadenylation during egg activation after fertilisation.[28]

Evolution

Polynucleotide phosphorylase is an enzyme that is part of the bacterial degradosome and archaeal exosome (two closely related complexes that recycle RNA into nucleotides). It evolved before the split between bacteria and archaea. This enzyme degrades RNA by attacking the bond between the 3'-most nucleotides with a phosphate, breaking off a diphosphate nucleotide. This reaction is reversible, and so the enzyme can also extend RNA with more nucleotides. The tails added by polynucleotide phosphorylase are very rich in adenine. The choice of adenine could be a result of higher ADP concentrations than other nucleotides as a result of using ATP as an energy currency, making it more likely to be incorporated in this tail in early lifeforms. It has been suggested that the involvement of adenine-rich tails in RNA degradation prompted the later evolution of polyadenylate polymerases (the enzymes that produce poly(A) tails with no other nucleotides in them).[29] Polyadenylate polymerases in both bacteria and eukaryotes have evolved from CCA-adding enzyme after the split between bacteria and archaea. CCA-adding enzyme is the enzyme that completes the 3' ends of tRNAs. Its catalytic domain is homologous to that of other polymerases.[4] Some lineages have not evolved polyadenylate polymerase, like archaea and cyanobacteria.[29]

References

  1. ^ a b Hunt AG, Xu R, Addepalli B; et al. (2008). "Arabidopsis mRNA polyadenylation machinery: Comprehensive analysis of protein-protein interactions and gene expression profiling". BMC Genomics. 9: 220. doi:10.1186/1471-2164-9-220. PMC 2391170. PMID 18479511. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  2. ^ Ford LP, Bagga PS, Wilusz J (1997). "The poly(A) tail inhibits the assembly of a 3'-to-5' exonuclease in an in vitro RNA stability system". Mol. Cell. Biol. 17 (1): 398–406. PMC 231764. PMID 8972220. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Régnier P, Arraiano CM (2000). "Degradation of mRNA in bacteria: Emergence of ubiquitous features". Bioessays. 22 (3): 235–44. doi:10.1002/(SICI)1521-1878(200003)22:3<235::AID-BIES5>3.0.CO;2-2. PMID 10684583. {{cite journal}}: Unknown parameter |month= ignored (help)
  4. ^ a b Martin G, Keller W (2007). "RNA-specific ribonucleotidyl transferases". RNA. 13 (11): 1834–49. doi:10.1261/rna.652807. PMC 2040100. PMID 17872511. {{cite journal}}: Unknown parameter |month= ignored (help)
  5. ^ Reinisch KM, Wolin SL (2007). "Emerging themes in non-coding RNA quality control". Curr. Opin. Struct. Biol. 17 (2): 209–14. doi:10.1016/j.sbi.2007.03.012. PMID 17395456. {{cite journal}}: Unknown parameter |month= ignored (help)
  6. ^ Dreyfus M, Régnier P (2002). "The poly(A) tail of mRNAs: Bodyguard in eukaryotes, scavenger in bacteria". Cell. 111 (5): 611–3. PMID 12464173. {{cite journal}}: Unknown parameter |month= ignored (help)
  7. ^ Saini HK, Griffiths-Jones S, Enright AJ (2007). "Genomic analysis of human microRNA transcripts". Proc. Natl. Acad. Sci. U.S.A. 104 (45): 17719–24. doi:10.1073/pnas.0703890104. PMC 2077053. PMID 17965236. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  8. ^ Erdmann VA, Szymanski M, Hochberg A, Groot N, Barciszewski J (2000). "Non-coding, mRNA-like RNAs database Y2K". Nucleic Acids Res. 28 (1): 197–200. doi:10.1093/nar/28.1.197. PMC 102406. PMID 10592224.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ a b Liu D, Brockman JM, Dass B; et al. (2007). "Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis". Nucleic Acids Res. 35 (1): 234–46. doi:10.1093/nar/gkl919. PMC 1802579. PMID 17158511. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  10. ^ van Helden J, del Olmo M, Pérez-Ortín JE (2000). "Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals". Nucleic Acids Res. 28 (4): 1000–10. PMC 102588. PMID 10648794. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  11. ^ Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D (2000). "Patterns of variant polyadenylation signal usage in human genes". Genome Res. 10 (7): 1001–10. PMC 310884. PMID 10899149. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  12. ^ Venkataraman K, Brown KM, Gilmartin GM (2005). "Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition". Genes Dev. 19 (11): 1315–27. doi:10.1101/gad.1298605. PMC 1142555. PMID 15937220. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  13. ^ a b Millevoi S, Loulergue C, Dettwiler S; et al. (2006). "An interaction between U2AF 65 and CF I(m) links the splicing and 3' end processing machineries". EMBO J. 25 (20): 4854–64. doi:10.1038/sj.emboj.7601331. PMC 1618107. PMID 17024186. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  14. ^ Glover-Cutter K, Kim S, Espinosa J, Bentley DL (2008). "RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes". Nat. Struct. Mol. Biol. 15 (1): 71–8. doi:10.1038/nsmb1352. PMID 18157150. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  15. ^ Balbo PB, Bohm A (2007). "Mechanism of poly(A) polymerase: Structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis". Structure. 15 (9): 1117–31. doi:10.1016/j.str.2007.07.010. PMC 2032019. PMID 17850751. {{cite journal}}: Unknown parameter |month= ignored (help)
  16. ^ Viphakone N, Voisinet-Hakil F, Minvielle-Sebastia L (2008). "Molecular dissection of mRNA poly(A) tail length control in yeast". Nucleic Acids Res. 36 (7): 2418–33. doi:10.1093/nar/gkn080. PMC 2367721. PMID 18304944. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  17. ^ Dichtl B, Blank D, Sadowski M, Hübner W, Weiser S, Keller W (2002). "Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination". EMBO J. 21 (15): 4125–35. PMC 126137. PMID 12145212. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  18. ^ Stumpf G, Domdey H (1996). "Dependence of yeast pre-mRNA 3'-end processing on CFT1: A sequence homolog of the mammalian AAUAAA binding factor". Science (journal). 274 (5292): 1517–20. PMID 8929410. {{cite journal}}: Unknown parameter |month= ignored (help)
  19. ^ LaCava J, Houseley J, Saveanu C; et al. (2005). "RNA degradation by the exosome is promoted by a nuclear polyadenylation complex". Cell. 121 (5): 713–24. doi:10.1016/j.cell.2005.04.029. PMID 15935758. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  20. ^ Steege DA (2000). "Emerging features of mRNA decay in bacteria". RNA. 6 (8): 1079–90. PMC 1369983. PMID 10943888. {{cite journal}}: Unknown parameter |month= ignored (help)
  21. ^ Shen Y, Ji G, Haas BJ; et al. (2008). "Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation". Nucleic Acids Res. 36 (9): 3150–61. doi:10.1093/nar/gkn158. PMC 2396415. PMID 18411206. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  22. ^ Yan J, Marr TG (2005). "Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat". Genome Res. 15 (3): 369–75. doi:10.1101/gr.3109605. PMC 551563. PMID 15741508. {{cite journal}}: Unknown parameter |month= ignored (help)
  23. ^ Shen Y, Ji G, Haas BJ; et al. (2008). "Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation". Nucleic Acids Res. 36 (9): 3150–61. doi:10.1093/nar/gkn158. PMC 2396415. PMID 18411206. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  24. ^ Wakiyama M, Takimoto K, Ohara O, Yokoyama S (2007). "Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system". Genes Dev. 21 (15): 1857–62. doi:10.1101/gad.1566707. PMC 1935024. PMID 17671087. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  25. ^ Shell SA, Hesse C, Morris SM, Milcarek C (2005). "Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection". J. Biol. Chem. 280 (48): 39950–61. doi:10.1074/jbc.M508848200. PMID 16207706. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  26. ^ Meijer HA, Bushell M, Hill K; et al. (2007). "A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells". Nucleic Acids Res. 35 (19): e132. doi:10.1093/nar/gkm830. PMC 2095794. PMID 17933768. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  27. ^ Wu L, Fan J, Belasco JG (2006). "MicroRNAs direct rapid deadenylation of mRNA". Proc. Natl. Acad. Sci. U.S.A. 103 (11): 4034–9. doi:10.1073/pnas.0510928103. PMC 1449641. PMID 16495412. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  28. ^ Cui J, Sackton KL, Horner VL, Kumar KE, Wolfner MF (2008). "Wispy, the Drosophila homolog of GLD-2, is required during oogenesis and egg activation". Genetics. 178 (4): 2017–29. doi:10.1534/genetics.107.084558. PMC 2323793. PMID 18430932. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  29. ^ a b Slomovic S, Portnoy V, Yehudai-Resheff S, Bronshtein E, Schuster G (2008). "Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases". Biochim. Biophys. Acta. 1779 (4): 247–55. doi:10.1016/j.bbagrm.2007.12.004. PMID 18177749. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)


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