The RNA helicase Ddx5/p68 binds to hUpf3 and enhances NMD of Ddx17/p72 and Smg5 mRNA

Non-sense-mediated mRNA decay (NMD) is a mechanism of translation-dependent mRNA surveillance in eukaryotes: it degrades mRNAs with premature termination codons (PTCs) and contributes to cellular homeostasis by downregulating a number of physiologically important mRNAs. In the NMD pathway, Upf proteins, a set of conserved factors of which Upf1 is the central regulator, recruit decay enzymes to promote RNA cleavage. In mammals, the degradation of PTC-containing mRNAs is triggered by the exon–junction complex (EJC) through binding of its constituents Upf2 and Upf3 to Upf1. The complex formed eventually induces translational repression and recruitment of decay enzymes. Mechanisms by which physiological mRNAs are targeted by the NMD machinery in the absence of an EJC have been described but still are discussed controversially. Here, we report that the DEAD box proteins Ddx5/p68 and its paralog Ddx17/p72 also bind the Upf complex by physical interaction with Upf3, thereby interfering with the binding of EJC. By activating the NMD machinery, Ddx5 is shown to regulate the expression of its own, Ddx17 and Smg5 mRNAs. For NMD triggering, the adenosine triphosphate-binding activity of Ddx5 and the 3′-untranslated region of substrate mRNAs are essential.     

Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72

RNA helicases, like their DNA-specific counterparts, can function as processive enzymes, unwinding RNA with a defined step size in a unidirectional fashion. Recombinant nuclear DEAD-box protein p68 and its close relative p72 are reported here to function in a similar fashion, though the processivity of both RNA helicases appears to be limited to only a few consecutive catalytic steps. The two proteins resemble each other also with regard to other biochemical properties. We have found that both proteins exhibit an RNA annealing in addition to their helicase activity. By using both these activities the enzymes are able in vitro to catalyse rearrangements of RNA secondary structures that otherwise are too stable to be resolved by their low processive helicase activities. RNA rearrangement proceeds via protein induced formation and subsequent resolution of RNA branch migration structures, whereby the latter step is dependent on ATP hydrolysis. The analysed DEAD-box proteins are reminiscent of certain DNA helicases, for example those found in bacteriophages T4 and T7, that catalyse homologous DNA strand exchange in cooperation with the annealing activity of specific single strand binding proteins.     

富含半胱氨酸分泌蛋白生物学功能的研究进展

富含半胱氨酸分泌蛋白(cysteine-rich secretory proteins,CRISPs)包含众多不同起源的蛋白质,其大部分成员功能未知。近年来研究发现,哺乳动物中的CRISP家族各成员主要存在于生殖道中,在精子的成熟、精卵融合以及免疫系统中发挥着非常重要的作用,并且其表达水平的改变与人类多种重大疾病密切相关,有望成为某些疾病理想的生物标记物和药物靶点;而非哺乳动物中的CRISP家族成员则主要存在于腺体的分泌液中,能够阻断Na+、K+、Ca2+及环核苷酸门控通道,并与炎症反应密切相关。近来,作者所在实验室从低等无颌类脊椎动物七鳃鳗的口腔腺中分离纯化出富含半胱氨酸分泌蛋白,其与CRISP家族成员具有较高的同源性。该文针对CRISP家族成员生物学功能的最新进展做了分析归纳,并指出了相关研究的发展趋势。     

The ATPase, RNA unwinding, and RNA binding activities of recombinant p68 RNA helicase

p68 RNA helicase, a nuclear RNA helicase, was identified 2 decades ago. The protein plays very important roles in cell development and organ maturation. However, the biological functions and enzymology of p68 RNA helicase are not well characterized. We report the expression and purification of recombinant p68 RNA helicase in a bacterial system. The recombinant p68 is an ATP-dependent RNA helicase. ATPase assays demonstrated that double-stranded RNA (dsRNA) is much more effective than single-stranded RNA in stimulating ATP hydrolysis by the recombinant protein. Consistently, RNA-binding assays showed that p68 RNA helicase binds single-stranded RNA weakly in an ATP-dependent manner. On the other hand, the recombinant protein has very high affinity for dsRNA. Binding of the protein to dsRNA is ATP-independent. The data indicate that p68 may directly target dsRNA as its natural substrate. Interestingly, the recombinant p68 RNA helicase unwinds dsRNA in both 3' --> 5' and 5' --> 3' directions. This is the second example of a Asp-Glu-Ala-Asp (DEAD) box RNA helicase that unwinds RNA duplexes in a bi-directional manner.     

Purification and Characterization of p68/70, Regeneration-Associated Proteins from Goldfish Brain

Abstract: Two acidic proteins (p68/70) previously shown to be associated with regeneration of the goldfish optic nerve were purified 887-fold from brain homogenates of Carassius auratus. Purification to homogeneity was achieved by sequential chromatography of a 100,000 g brain supernatant fraction on DEAE-Sephacel, Cu²⁺-charged iminodiacetic acid agarose, and gel filtration. The Stokes radius of the doublet was determined to be 5.8 nm, and the sedimentation coefficient calculated to be 5 2. From these values a molecular mass of 128 kDa and a frictional coefficient ratio of 1.6 were calculated. Chromatofocusing on a high-resolution DEAE column resolved the protein doublet into three dimeric species of p68, p68/70, and p70. These results indicate that the proteins are highly elongated and associate as homodimers or as a hetero-dimer. Subcellular localization and membrane extraction experiments indicated p68/70 to be a component of the plasma membrane associated primarily through hydro-phobic interactions. p68/70 demonstrated biphasic behavior in phase partition experiments using Triton 114. Analysis of hydrolytic products indicated p68/70 to be a glyco-protein, containing 11% carbohydrate.     

缓步动物热溶性蛋白的独有特性及其在极端环境适应中的功能

缓步动物（tardigrades，俗称水熊虫）等一些低等动物可在干燥、低温、低压等极端条件下长期生存。这种超常的生存能力依赖于细胞在大幅度脱水后，进入一种叫做隐生（cryptobiosis）的特殊状态，使细胞脱水、身体萎缩并停止新陈代谢，从而可以允许动物在极端条件下生存多年。当环境好转时，处于隐生状态的细胞或者身体又可以再次吸收水份进行复苏。缓步动物中有着多种独特的内在无序蛋白质（intrinsic disorder protein），统称为热溶性蛋白质。这些热溶性蛋白质在细胞脱水过程中构象发生重要变化，可对液态水进行固定，从而起到了重要的细胞保护作用。对此类蛋白质的性质研究尚处于初期阶段，缺乏深入的机理性研究。本文简要总结了缓步动物中特有热溶性蛋白质的序列特征、理化性质，及其潜在的生物功能与机制。同时讨论了这些热溶性蛋白质在高等动物细胞对低温、低氧等极端环境适应中的可能应用。人类细胞在极端环境中的隐生和可逆复苏，将在医学领域和未来宇宙探索与星际移民中有极其重要的用途。     

The DEAD box proteins DDX5 (p68) and DDX17 (p72): Multi-tasking transcriptional regulators

Members of the DEAD box family of RNA helicases, which are characterised by the presence of twelve conserved motifs (including the signature D-E-A-D motif) within a structurally conserved ‘helicase’ core, are involved in all aspects of RNA metabolism. Apart from unwinding RNA duplexes, which established these proteins as RNA helicases, DEAD box proteins have been shown to also catalyse RNA annealing and to displace proteins from RNA. DEAD box proteins generally act as components of large multi-protein complexes and it is thought that interactions, via their divergent N- and C-terminal extensions, with other factors in the complexes may be responsible for the many different functions attributed to these proteins.     

Protein SRP68 of human signal recognition particle: identification of the RNA and SRP72 binding domains

The signal recognition particle (SRP) plays an important role in the delivery of secretory proteins to cellular membranes. Mammalian SRP is composed of six polypeptides among which SRP68 and SRP72 form a heterodimer that has been notoriously difficult to investigate. Human SRP68 was purified from overexpressing Escherichia coli cells and was found to bind to recombinant SRP72 as well as in vitro-transcribed human SRP RNA. Polypeptide fragments covering essentially the entire SRP68 molecule were generated recombinantly or by proteolytic digestion. The RNA binding domain of SRP68 included residues from positions 52 to 252. Ninety-four amino acids near the C terminus of SRP68 mediated the binding to SRP72. The SRP68-SRP72 interaction remained stable at elevated salt concentrations and engaged approximately 150 amino acids from the N-terminal region of SRP72. This portion of SRP72 was located within a predicted tandem array of four tetratricopeptide (TPR)-like motifs suggested to form a superhelical structure with a groove to accommodate the C-terminal region of SRP68.