Sandbox RDE-1

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Revision as of 04:11, 9 October 2018

Introduction

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The rde-1 gene is a member of the Argonaute gene family. Proteins from "Argonaute" family form an evolutionarily conserved family whose members silence gene expression in pathways such as RNA interference (RNAi). Argonaute family proteins can be divided into two types, AGO and Piwi proteins, depending on the small RNA they bonded to. Both types of Argonaute proteins bind 21–35 nucleotide-long small RNA guides whose sequence identifies the genes to be silenced.^[1] RDE-1 (RNAi-DEfective 1), a primary Argonaute protein, is required for RNA-mediated interference in Caenorhabditis elegans; thus, it is also known as RNAi promoting factor. Its gene locus was first characterized in C. elegans mutants resistant to RNAi, and was found to be a member of the Piwi gene family that includes plant, Drosophila, and vertebrate homologs.^[2]

1 Structure
2 Function
3 Importance
4 References

Structure

All "Argonaute"/Piwi proteins possess three primary domains forming a crescent-shaped base: the PAZ, MID, and PIWI domains. The amino-terminal PAZ domain uses its oligonucleotide-binding (OB) fold to secure the 3′ end of the small RNA guide strand to Argonaute protein. A conserved hydrophobic cavity within the PAZ domain recognizes the characteristic two-nucleotide, 3′ overhanging end of the guide-passenger siRNA generated by Dicer. The MID domain anchors the 5′ monophosphate of a siRNA to the Argonaute protein, securing the guide through multiple cycles of target cleavage. In vitro, studies suggest that 5′ phosphate binding helps align the small RNA on the surface of "Argonaute" protein, ensuring that the correct bond of the target is positioned in the endonuclease active site.^[1] In other words, the PAZ and MID domains orient and anchor the double-stranded siRNA by binding to the 3’ and 5’ termini, respectively, leaving the internal nucleotides accessible for base pairing.^[1]^[3] The carboxy-terminal PIWI domain resembles nuclease RNase H in which it folds into an RNase H-like structure. In RDE-1, this domain contains three conserved amino acids, aspartate-aspartate-histidine, that form a catalytic triad "DDH".^[3] The crystal structure of RDE-1 has not been fully elucidated, but can be assumed to closely resemble its human homologs. The full length of RDE-1 protein is 1020 amino acids (aa)^[2] in which about 110 of those aa makes up the PAZ domain and 300 aa makes up the PIWI domain.^[4]

Function

Proposed RNAi pathway for exogenous trigger dsRNA in C. elegans.^[5]

RDE-1 is not required for the initial processing of the trigger RNA into siRNAs in RNAi, but it is required in the effector step.^[6] The trigger dsRNA is bound by RDE-4 onto a Dicer complex and this complex cleaves the dsRNA into 21-25nt primary siRNA. The siRNA binds to RDE-1 promoting the formation of the RNA-induced silencing complex (RISC) and RDE-1 shuttles the siRNA to that effector complex.^[7]^[8] The RNase H activity in PIWI domain in RDE-1 facilitates siRNA maturation, cleaving siRNA into a single stranded siRNA or guide RNA^[9] while RISC is activated when ATP is added to the complex and utilized the guide RNA on RDE-1 to base pair with the target transcript.^[8] The activation of RISC promotes the recruitment of RNA-dependent RNA polymerase (RdRP) which triggers the amplification of the secondary siRNAs to exhibit target transcript degradation.^[10]

Importance

Mutation of any residues in the RNase H catalytic triad abolishes Slicer activity in human Argonaute protein Ago2, suggesting that the RNase H domain is directly responsible for target mRNA degradation.^[11] However, RDE-1 has not been implicated in mRNA-cleavage activity.

Instead, RDE-1 with mutations in the conserved DDH motif exhibit reduced passenger (sense) strand turnover, suggesting that RNase H activity serves to cleave the passenger strand, leaving the guide (antisense) strand accessible for base-pairing to target mRNA.^[9] Further, target silencing can be fully restored in DDH motif mutants by loading single-stranded siRNA, suggesting that a downstream component in the RNAi pathway is responsible for Slicer activity.^[9] Thus, RDE-1’s RNase H domain facilitates siRNA maturation but is not directly involved in cleaving target mRNA transcripts.

RDE-1 is important for cleavage of the passenger strand and shuttling the siRNA to the appropriate RISC in C. elegans.^[9]^[8] Without RDE-1, RISC cannot obtain the guide RNA for identifying the target transcript and thus transcript degradation cannot process properly or not at all. This protein is therefore also important for silencing a disease-causing gene by degradation of mRNA.^[8]

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References

↑ ^1.0 ^1.1 ^1.2 Cenik ES, Zamore PD. Argonaute proteins. Curr Biol. 2011 Jun 21;21(12):R446-9. doi: 10.1016/j.cub.2011.05.020. PMID:21683893 doi:http://dx.doi.org/10.1016/j.cub.2011.05.020
↑ ^2.0 ^2.1 Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell. 1999 Oct 15;99(2):123-32. PMID:10535731
↑ ^3.0 ^3.1 Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29. PMID:15284453 doi:10.1126/science.1102514
↑ Cerutti L, Mian N, Bateman A. Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends Biochem Sci. 2000 Oct;25(10):481-2. doi: 10.1016/s0968-0004(00)01641-8. PMID:11050429 doi:http://dx.doi.org/10.1016/s0968-0004(00)01641-8
↑ https://en.wikipedia.org/wiki/RDE-1#/media/File:Exogenous_RNAi_Pathway_in_C._elegans,_edited.svg
↑ Parrish S, Fire A. Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. RNA. 2001 Oct;7(10):1397-402. PMID:11680844
↑ Tabara H, Yigit E, Siomi H, Mello CC. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell. 2002 Jun 28;109(7):861-71. doi: 10.1016/s0092-8674(02)00793-6. PMID:12110183 doi:http://dx.doi.org/10.1016/s0092-8674(02)00793-6
↑ ^8.0 ^8.1 ^8.2 ^8.3 Hannon GJ. RNA interference. Nature. 2002 Jul 11;418(6894):244-51. doi: 10.1038/418244a. PMID:12110901 doi:http://dx.doi.org/10.1038/418244a
↑ ^9.0 ^9.1 ^9.2 ^9.3 Steiner FA, Okihara KL, Hoogstrate SW, Sijen T, Ketting RF. RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans. Nat Struct Mol Biol. 2009 Feb;16(2):207-11. doi: 10.1038/nsmb.1541. Epub 2009 Jan, 18. PMID:19151723 doi:http://dx.doi.org/10.1038/nsmb.1541
↑ Boisvert ME, Simard MJ. RNAi pathway in C. elegans: the argonautes and collaborators. Curr Top Microbiol Immunol. 2008;320:21-36. doi: 10.1007/978-3-540-75157-1_2. PMID:18268838 doi:http://dx.doi.org/10.1007/978-3-540-75157-1_2
↑ Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004 Sep 3;305(5689):1437-41. Epub 2004 Jul 29. PMID:15284456 doi:http://dx.doi.org/10.1126/science.1102513

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@@ Line 1: / Line 1: @@
 == Introduction ==
-<Structure load='4krf' size='350' frame='true' align='right' caption='Protein length: 1020 aa, Mass: 118,804 Da' scene='Insert optional scene name here' />
+<Structure load='4krf' size='350' frame='true' align='right' caption='Structure of Human Argonaute-1 let-7 complex as representation of RDE-1 since they have similar function. Thus, this complex is a model for Argonaute proteins in general.<ref> PMID: 23746446</ref>' scene='Insert optional scene name here' />
 The rde-1 gene is a member of the ''Argonaute'' gene family. Proteins from "Argonaute" family form an evolutionarily conserved family whose members silence gene expression in pathways such as RNA interference (RNAi). Argonaute family proteins can be divided into two types, AGO and Piwi proteins, depending on the small RNA they bonded to. Both types of Argonaute proteins bind 21–35 nucleotide-long small RNA guides whose sequence identifies the genes to be silenced.<ref name=four/>
 '''RDE-1''' (RNAi-DEfective 1), a primary Argonaute protein, is required for RNA-mediated interference in ''Caenorhabditis elegans''; thus, it is also known as RNAi promoting factor. Its gene locus was first characterized in ''C. elegans'' mutants resistant to RNAi, and was found to be a member of the Piwi gene family that includes plant, Drosophila, and vertebrate homologs.<ref name=two>PMID: 10535731</ref>
@@ Line 8: / Line 8: @@
 == Function ==
-[[Image:RDE-1 Proposed Fxn.png|300px||left|thumb|Proposed RNAi pathway for exogenous trigger dsRNA in C. elegans.<ref>https://en.wikipedia.org/wiki/RDE-1#/media/File:Exogenous_RNAi_Pathway_in_C._elegans,_edited.svg</ref>]] '''RDE-1''' is not required for the initial processing of the trigger RNA into siRNAs in RNAi, but it is required in the effector step.<ref>PMID: 11680844</ref> The trigger dsRNA is bound by RDE-4 onto a '''Dicer''' complex and this complex cleaves the dsRNA into 21-25nt primary siRNA. The siRNA binds to RDE-1 promoting the formation of the RNA-induced silencing complex (RISC) and RDE-1 shuttles the siRNA to that effector complex.<ref name=promo>DOI: 10.1016/S0092-8674(02)00793-6</ref><ref name=shuttle>PMID: 12110901</ref> The RNase H activity in PIWI domain in RDE-1 facilitates siRNA maturation, cleaving siRNA into a single stranded siRNA or guide RNA<ref name=cleave>DOI: 10.1038/nsmb.1541</ref> while RISC is activated when ATP is added to the complex and utilized the guide RNA on RDE-1 to base pair with the target transcript.<ref name=shuttle/> The activation of RISC promotes the recruitment of RNA-dependent RNA polymerase (RdRP) which triggers the amplification of the secondary siRNAs to exhibit target transcript degradation.<ref>DOI: 10.1007/978-3-540-75157-1_2</ref>
+[[Image:RDE-1 Proposed Fxn.png|300px||left|thumb|Proposed RNAi pathway for exogenous trigger dsRNA in C. elegans.<ref>https://en.wikipedia.org/wiki/RDE-1#/media/File:Exogenous_RNAi_Pathway_in_C._elegans,_edited.svg</ref>]] RDE-1 is not required for the initial processing of the trigger RNA into siRNAs in RNAi, but it is required in the effector step.<ref>PMID: 11680844</ref> The trigger dsRNA is bound by RDE-4 onto a '''Dicer''' complex and this complex cleaves the dsRNA into 21-25nt primary siRNA. The siRNA binds to RDE-1 promoting the formation of the RNA-induced silencing complex (RISC) and RDE-1 shuttles the siRNA to that effector complex.<ref name=promo>DOI: 10.1016/S0092-8674(02)00793-6</ref><ref name=shuttle>PMID: 12110901</ref> The RNase H activity in PIWI domain in RDE-1 facilitates siRNA maturation, cleaving siRNA into a single stranded siRNA or guide RNA<ref name=cleave>DOI: 10.1038/nsmb.1541</ref> while RISC is activated when ATP is added to the complex and utilized the guide RNA on RDE-1 to base pair with the target transcript.<ref name=shuttle/> The activation of RISC promotes the recruitment of RNA-dependent RNA polymerase (RdRP) which triggers the amplification of the secondary siRNAs to exhibit target transcript degradation.<ref>DOI: 10.1007/978-3-540-75157-1_2</ref>
 == Importance ==

Sandbox RDE-1

From Proteopedia

Revision as of 04:11, 9 October 2018

Introduction

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Structure

Function

Importance

References

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