Nucleic Acids Res.
January 1, 2006;
Xp54 and related (DDX6-like) RNA helicases: roles in messenger RNP assembly, translation regulation and RNA degradation.
The DEAD-box RNA helicase Xp54
is an integral component of the messenger ribonucleoprotein (mRNP) particles of Xenopus oocytes. In oocytes, several abundant proteins bind pre-mRNA transcripts to modulate nuclear export, RNA stability and translational fate. Of these, Xp54
, the mRNA-masking protein FRGY2
and its activating protein kinase CK2alpha, bind to nascent transcripts on chromosome loops, whereas an Xp54
-associated factor, RapA/B, binds to the mRNP complex in the cytoplasm. Over-expression, mutation and knockdown experiments indicate that Xp54
functions to change the conformation of mRNP complexes, displacing one subset of proteins to accommodate another. The sequence of Xp54
is highly conserved in a wide spectrum of organisms. Like Xp54
, Drosophila Me31B and Caenorhabditis CGH-1 are required for proper meiotic development, apparently by regulating the translational activation of stored mRNPs and also for sorting certain mRNPs into germplasm-containing structures. Studies on yeast Dhh1 and mammalian rck/p54 have revealed a key role for these helicases in mRNA degradation and in earlier remodelling of mRNP for entry into translation, storage or decay pathways. The versatility of Xp54
and related helicases in modulating the metabolism of mRNAs at all stages of their lifetimes marks them out as key regulators of post-transcriptional gene expression.
Nucleic Acids Res.
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Figure 1. Alignment of the amino acid sequences of eight members of the DDX6 subfamily of DEAD-box RNA helicases. Identical residues (asterisk) and conserved substitutions (colon or stop) are indicated. Alignments were made using the Clustal W algorithm. Conserved motifs, shared by other DEAD-box helicases are highlighted (red). N-terminal extensions (green) or C-terminal extensions (orange) are present in only some members. In Xp54, single residues, S or T (yellow), are indicated as potential phosphorylation sites. Basic residues acting as an NLS are highlighted (blue) as are residues constituting a leucine-rich NES (purple). Extent of the two RecA-like domains are indicated by arrows: domain 1 (brown), domain 2 (pink).
Figure 2. Diagram showing the location of sequence motifs and proposed functional regions within Xp54. Blocks indicate the conserved DEAD-box helicase motifs (red), the N-terminal region with a high content of glycine and glutamine residues (GQ-rich; green), the putative NLS (blue), the identified NES (purple) and putative acidophilic protein kinase (PK) sites (yellow). Functional analysis was carried out using vectors expressing truncations of recombinant Xp54 (17).
Figure 3. Diagram indicating possible interactions of mRNA-bound and associated proteins involved with Xp54 helicase in the remodelling of mRNP for storage, translation and degradation. FRGY2 is the major mRNA masking protein that avidly binds single-stranded RNA. Stability of RNA binding is maintained by continuous phosphorylation (P red) of FRGY2 oligomers by CK2α, which is an integral component of stored mRNP particles. The RNA helicase Xp54 can be efficiently crosslinked to an abundant mRNP component Rap, which is an RNA-associated protein that may regulate helicase activity. Furthermore, translation repression may involve formation of a 3′–5′ molecular bridge between the protein that binds to the cytoplasmic polyadenylation element (CPEB), oligomerized Xp54 and the cap-binding protein eIF4E. The eIF4E regulatory protein 4E-T may be required to complete the bridge. In translation activation, the poly(A) tail is generally extended and most, but not all, of FRGY2 is released from the mRNA, apparently through interaction with the acidic chaperone, nucleoplasmin (51) and/or phosphorylation by the protein kinase Akt (52). In addition, the translation initiation factor eIF4G may displace the co-repressor 4E-T and form a bridge with poly(A)-binding protein bound to the extended tail (data not shown). Coincident with translation activation is phosphorylation of Xp54 (P red) by an unidentified protein kinase (PK). During mRNA degradation, studies on other systems (71) indicate that deadenylation is followed by decapping (Dcp1/2) and exonuclease digestion by Xrn1 (data not shown).
Figure 4. Diagram showing the location of sequence motifs and proposed functional regions within Xenopus RapA and RapB which are members of the Scd6p family. Blocks indicate the conserved Sm-I and Sm-II motifs (orange) that constitute the Sm-like domain, the conserved FDF domain (pink) and the more variable blocks of RGG repeats (green), serine/threonine-rich regions (yellow) and proline-rich regions (violet). RAPA and RAPB genes are differentially expressed during oogenesis: RAPA during early oogenesis when mRNP synthesis is maximum, RAPB throughout oogenesis and into early embryogenesis when maternal mRNAs are being translated and degraded.
Figure 5. Major pathways involving DDX6-like helicases in the metabolism of mRNA of different organisms. Different aspects of helicase activity are emphasized in different organisms. In S.cerevisiae, best studied is the decay pathway in which Dhh1p has been shown to associate both with the mRNA deadenylation complex containing Ccr4p and Pop2p and the mRNA decapping complex containing Dcp1/2p, Pat1p and Lsm1-7p. Decapping activity is located in P-bodies. Deletion of DHH1 results in a block in meiosis. In Caenorhabditis, CGH-1 locates to cytoplasmic mRNP particles and to P granules. Whereas CGH-1 particles are dynamic structures responsive to meiotic development, P granules may represent sites of mRNP assembly or remodelling. CEY2-4 are CSD proteins associated with mRNA. Deletion of CGH-1 results in physiological germ cell apoptosis. In Drosophila, Me31B binds to maternal mRNAs synthesized in nurse cells. Including the CSD protein Yps and the mRNA-localization factor Exu, mRNP is exported to the oocyte where localization between anterior (A) and posterior (P) regions may occur. In addition, Me31B locates to sponge bodies, which may represent the site of germplasm. Deletion of ME31B results in premature translation of mRNAs, normally located to and stored in the oocyte, in nurse cells. In Xenopus, Xp54 can shuttle between cytoplasm and nucleus (GV) but, after binding to nascent pre-mRNA transcripts together with the CSD protein FRGY2, exits the nucleus in mRNP particles, most of these being stored in a non-translating (maternal) form. In early oocytes, Xp54 also locates to the Balbiani body that contains the germplasm. In mammalian cells, rck/p54 is bound to mRNA together with the CSD protein YB1/p50. Some mRNP may be held in a non-translating form. rck/p54 is also a component of SGs and is implicated in the remodelling of mRNP for translation, storage or degradation in P-bodies. mRNP marked for degradation is associated with the decapping enzymes Dcp1/2 and the mRNA may be eventually degraded by the 5′ exonuclease Xrn1. For references see text.