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Autor     Scott M. Hammond
Titel    Dicing and slicing - The core machinery of the RNA interference pathway
Zeitschrift    FEBS Letters
Ausgabe    579
Jahr    2005
Seiten    5822–5829
URL    http://www.sciencedirect.com/science/article/pii/S0014579305010884

Literaturverz.   

ja
Fußnoten    nein
Fragmente    5


Fragmente der Quelle:
[1.] Ww/Fragment 008 22 - Diskussion
Zuletzt bearbeitet: 2014-10-29 05:58:09 Hindemith
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The goal of the initiation step of RNAi is the generation of siRNAs from long dsRNAs or mature miRNAs from their primary transcripts. This is achieved by the action of two families of RNase III-dependent genes, Dicer and Drosha. RNase III enzymes fall into three classes (Nicholson, 2003). Class I enzymes, found in bacteria and yeast, contain a single RNase III domain joined to a dsRBD (dsRNA binding domain proteins). Class II and III enzymes contain two RNase III catalytic domains. Class III enzymes are further characterized [by a helicase domain and a PAZ (Piwi/Argonaute/Zwille) domain.] The goal of the initiator step of RNAi is the generation of siRNAs from long dsRNAs, or mature microRNAs from their primary transcripts. This is achieved by the action of two families of RNase III genes, Dicer and Drosha.

[Seite 5823]

RNaseIII enzymes fall into three classes (see Fig. 1, [11] for a review). Class I enzymes, found in bacteria and yeast, contain a single RNaseIII domain joined to a dsRBD. Class II and III enzymes contain two RNaseIII catalytic domains. Class III enzymes are further characterized by a helicase domain and a PAZ (Piwi/Argonaute/Zwille) domain.


[11] Nicholson, A.W. (2003) The ribonuclease III superfamily: forms and functions in RNA maturation, decay, and gene silencing (Hannon, G.J., Ed.), RNAi: A Guide to Gene Silencing, vol. 8, pp. 149–174, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

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[2.] Ww/Fragment 010 01 - Diskussion
Zuletzt bearbeitet: 2016-01-20 18:13:48 Schumann
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[Class III enzymes are further characterized] by a helicase domain and a PAZ (Piwi/Argonaute/Zwille) domain. This last domain is also present in Argonaute family proteins, already known to be essential for RNAi, which led to the proposal that Class III enzymes are the initiator of RNAi (Bass, 2000).

The generation of a siRNA from dsRNA potentially requires four endonucleolytic reactions. It has been revealed that Dicer acts as a monomer, using two endonucleolytic reactions to generate one new terminus (Zhang et al, 2004). This would occur if Dicer binds to an existing terminus and makes a cut ~21 nucleotides from the end (Schütze, 2004). If however the enzyme can not initiate processing from the end and is forced to cut internally, the reaction becomes significantly delayed. Once binding of Dicer occurred and a single new terminus is created, further processing occurrs at normal rates, since the enzyme now has terminal ends from which to process.

MicroRNAs (miRNAs) are transcribed by RNA polymerase II as long primary transcripts (Kim, 2005). The active miRNA species, termed the mature RNA, is present in a stem–loop structure within the primary transcript. The stem–loop can be located in an exon or in an intron. For example, the miRNAs miR-106b, miR-93, and miR-25 are located within an intron of the protein coding gene mcm-7. After transcription, the miRNAs are processed from the primary transcript, and the spliced mRNA is exported and translated . Sequential processing of the primary transcript by the RNase III enzymes Drosha and Dicer liberates the mature RNA. Drosha cleavage releases the stem–loop, termed the precursor, which is exported from the nucleus in an exportin-5/RAN-GTPase-dependent manner. In the cytoplasm, the precursor is processed into a siRNA-like structure by Dicer. Drosha generates a 2 nt 3’ overhang terminus on the precursor which is recognized by the PAZ domain of Dicer, analogous to the recognition of dsRNA termini. The double stranded miRNA is incorporated into RISC in a similar manner as siRNAs.

Drosha is a Class II enzyme. This enzyme assumes a pseudo-dimer catalytic [core similar to Dicer (Han et al, 2004).]

Class III enzymes are further characterized by a helicase domain and a PAZ (Piwi/Argonaute/Zwille) domain. This last domain is also present in Argonaute family proteins, already known to be essential for RNAi, which led to the proposal that Class III enzymes are the initiator of RNAi [12,13]. [...]

The generation of an siRNA from dsRNA potentially requires four endonucleolytic reactions. How does Dicer achieve this? Early models were based on the prediction that Dicer forms a dimer on the substrate and performs four cleavage reactions [15]. Recent data, however, favors a model whereby Dicer acts as a monomer, using two endonucleolytic reactions to generate one new terminus [16,17]. This would occur if Dicer bound to an existing terminus and made a cut ~21 nucleotides from the end. This was first suggested by studies using dsRNA substrates with blocked termini [16]. If the enzyme could not initiate processing from the end and was forced to process internally, the reaction was significantly delayed. The authors' interpretation was that internal binding was less efficient and caused a lag in processing. Once binding occurred and a single new terminus was created, further processing occurred at normal rates, since the enzyme now had terminal ends from which to process.

[Seite 5824]

MicroRNAs are transcribed from RNA polymerase II as long primary transcripts (see [26] for a review). The active microRNA species, termed the mature RNA, is present in a stem–loop structure within the primary transcript. The stem–loop can be located in an exon or an intron. For example, the microRNAs miR-106b, miR-93, and miR-25 are located within an intron of the protein coding gene mcm-7. After transcription, the microRNAs are processed out of the primary transcript, and the spliced mRNA is exported and translated. Whether the microRNA is processed before, during, or after splicing is not known. Sequential processing of the primary transcript by the RNaseIII enzymes Drosha and Dicer liberates the mature RNA. Drosha cleavage releases the stem–loop, termed the precursor, which is exported from the nucleus in an Exportin-5/RAN-GTPase-dependent manner. In the cytoplasm, the precursor is processed into a siRNA-like structure by Dicer. Drosha generates a 2 nt 30 overhang terminus on the precursor which is recognized by the PAZ domain of Dicer, analogous to the recognition of dsRNA termini. The doublestranded microRNA is incorporated into RISC in a similar manner as siRNAs.

Drosha is a Class II enzyme as shown in Fig. 1. This enzyme assumes a pseudo-dimer catalytic core similar to Dicer [27].


[12] Tabara, H., Sarkissian, M., Kelly, W.G., Fleenor, J., Grishok, A., Timmons, L., Fire, A. and Mello, C.C. (1999) The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132.

[13] Bass, B.L. (2000) Double-stranded RNA as a template for gene silencing. Cell 101, 235–238.

[14] Bernstein, E., Caudy, A.A., Hammond, S.M. and Hannon, G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366.

[15] Zamore, P.D. (2001) Thirty-three years later, a glimpse at the ribonuclease III active site. Mol. Cell 8, 1158–1160.

[16] Zhang, H., Kolb, F.A., Brondani, V., Billy, E. and Filipowicz, W. (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885.

[17] Zhang, H., Kolb, F.A., Jaskiewicz, L., Westhof, E. and Filipowicz, W. (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57–68.

[26] Kim, V.N. (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell. Biol. 6, 376–385.

[27] Han, J., Lee, Y., Yeom, K.H., Kim, Y.K., Jin, H. and Kim, V.N. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027.

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[3.] Ww/Fragment 011 01 - Diskussion
Zuletzt bearbeitet: 2014-10-29 07:42:22 Hindemith
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[Drosha is a Class II enzyme. This enzyme assumes a pseudo-dimer catalytic] core similar to Dicer (Han et al, 2004). The substrates of Drosha, miRNA primary transcripts, are structurally distinct from Dicer substrates. Drosha does not process from a dsRNA terminus. Rather, data suggests that primarily the stem–loop structure is recognized. In particular, the loop size appears to be important for recognition (Zeng et al, 2005). In addition, unstructured sequences flanking the stem–loop are essential for processing (Chen et al, 2004; Zeng et al, 2005). It is not evident how Drosha is able to recognize these sequences, as they are outside of the dsRNA stem. Possibly other unidentified cofactors play a role. Conserved sequence elements have been found in flanking regions of C. elegans miRNAs (Ohler et al, 2004). Drosha is a Class II enzyme as shown in Fig. 1. This enzyme assumes a pseudo-dimer catalytic core similar to Dicer [27]. The substrate of Drosha, microRNA primary transcripts, is structurally distinct from Dicer substrates. Drosha does not process from a dsRNA terminus. Rather, data suggests that the stem–loop structure is recognized. In particular, the loop size appears to be important for recognition [28]. In addition, unstructured sequences flanking the stem–loop are essential for processing [29,30]. It is not evident how Drosha would recognize these sequences, as they are outside of the dsRNA stem. Possibly other, unidentified cofactors play a role. Conserved sequence elements have been found in flanking regions of C. elegans microRNAs [31].

[27] Han, J., Lee, Y., Yeom, K.H., Kim, Y.K., Jin, H. and Kim, V.N. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027.

[28] Zeng, Y., Yi, R. and Cullen, B.R. (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24, 138–148.

[29] Chen, C.Z., Li, L., Lodish, H.F. and Bartel, D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86.

[30] Zeng, Y. and Cullen, B.R. (2005) Efficient processing of primary microRNA hairpins by Drosha requires flanking non-structured RNA sequences. J. Biol. Chem..

[31] Ohler, U., Yekta, S., Lim, L.P., Bartel, D.P. and Burge, C.B. (2004) Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10, 1309–1322

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[4.] Ww/Fragment 011 25 - Diskussion
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Chromatographic purification of RISC nuclease activity from Drosophila cells revealed several RISC components. The first identified component was Argonaute2 (Ago2) (Hammond et al, 2001). This protein is a member of a gene family conserved in most eukaryotic and several prokaryotic genomes. The C. elegans homolog, rde-1, was previously identified in a genetic screen for RNAi-deficient mutants, reinforcing its connection with RNAi (Tabara et al, [1999).] Chromatographic purification of RISC nuclease activity from Drosophila cells revealed several RISC components. The first identified component was Argonaute2 (Ago2) [43]. This protein is a member of a gene family conserved in most eukaryotic and several prokaryotic genomes. The C. elegans homolog, rde-1, was previously identified in a genetic screen for RNAi-deficient mutants, reinforcing its connection with RNAi [12].

[12] Tabara, H., Sarkissian, M., Kelly, W.G., Fleenor, J., Grishok, A., Timmons, L., Fire, A. and Mello, C.C. (1999) The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132.

[43] Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R. and Hannon, G.J. (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150

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[5.] Ww/Fragment 012 01 - Diskussion
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Structurally, this protein family is characterized by two domains, the PAZ domain and the PIWI domain. Structures for both domains have been solved. Additional RISC components with unknown roles in RNAi have also been identified. These include the RNA binding protein VIG, the Drosophila homolog of the Fragile X protein, dFXR, helicase proteins, and Tudor-SN (Ishizuka et al, 2002; Caudy et al, 2003). This last protein has five staphylococcal nuclease (SNase) domains and a Tudor domain. In humans, there are four closely related Argonaute family members, named Ago1-4. All four bind siRNAs and miRNAs at similar levels, and are widely expressed. Only Ago2, however, is present in a cleavage-competent RISC-complex (Meister et al, 2004). Similarly, siRNA-mediated knockdown, or targeted knockout, of Ago2 impaired RNAi of a reporter, while knockdown of Ago1, 3, 4 had no effect. The crystal structure of an Argonaute family member from Pyrococcus furiosus has been revealed (Song et al, 2004). The structure displayed an RNaseH fold for the signature PIWI domain. The crystal structure of a second archaean argonaute, Archaeoglobus fulgidus Piwi (AfPiwi), confirmed the RNaseH fold (Parker et al, 2004). The final demonstration that Slicer activity was contained within Ago2 was the reconstitution of minimal RISC with bacterially expressed, purified Ago2 and a single-stranded siRNA (Rivas et al, 2005). Structurally, this protein family is characterized by two domains, the PAZ domain and the PIWI domain. Structures for both domains have been solved (see below). Additional RISC components with unknown roles in RNAi

[5826:]

have also been identified. These include the RNA binding protein VIG, the Drosophila homolog of the Fragile X protein, dFXR, helicase proteins, and Tudor-SN [46–48]. This last protein has five staphylococcal nuclease (SNase) domains and a Tudor domain. [...]

[...]

[...] In humans, there are four closely related Argonaute family members, named Ago1-4. All four bind siRNAs and microRNAs at similar levels, and are widely expressed. Only Ago2, however, is present in a cleavage- competent RISC [52,53]. Similarly, siRNA-mediated knockdown, or targeted knockout, of Ago2 impairs RNAi of a reporter, while knockdown of Ago1, 3, 4 had no effect. These data can be interpreted in two ways: Ago2 alone is capable of interacting with Slicer, or Ago2 itself is Slicer. The answer was provided by the crystal structure of an Argonaute family member from Pyrococcus furiosus [54]. The structure revealed an RNaseH fold for the signature PIWI domain. The crystal structure of a second archaean Argonaute, Archaeoglobus fulgidus Piwi (AfPiwi), confirmed the RNaseH fold [55]. The final demonstration that Slicer activity was contained within Ago2 was the reconstitution of minimal RISC with bacterially expressed, purified Ago2 and a single-stranded siRNA [45].


[46] Caudy, A.A., Myers, M., Hannon, G.J. and Hammond, S.M. (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16, 2491–2496.

[47] Caudy, A.A. et al. (2003) A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414.

[48] Ishizuka, A., Siomi, M.C. and Siomi, H. (2002) A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev. 16, 2497–2508.

[52] Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G. and Tuschl, T. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197.

[53] Liu, J. et al. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441.

[54] Song, J.J., Smith, S.K., Hannon, G.J. and Joshua-Tor, L. (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434–1437.

[55] Parker, J.S., Roe, S.M. and Barford, D. (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 23, 4727–4737.

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