Prevalent RNA recognition motif duplication in the human genome

The sequence-specific recognition of RNA by proteins is mediated through various RNA binding domains, with the RNA recognition motif (RRM) being the most frequent and present in >50% of RNA-binding proteins (RBPs). Many RBPs contain multiple RRMs, and it is unclear how each RRM contributes to the binding specificity of the entire protein. We found that RRMs within the same RBP (i.e., sibling RRMs) tend to have significantly higher similarity than expected by chance. Sibling RRM pairs from RBPs shared by multiple species tend to have lower similarity than those found only in a single species, suggesting that multiple RRMs within the same protein might arise from domain duplication followed by divergence through random mutations. This finding is exemplified by a recent RRM domain duplication in DAZ proteins and an ancient duplication in PABP proteins. Additionally, we found that different similarities between sibling RRMs are associated with distinct functions of an RBP and that the RBPs tend to contain repetitive sequences with low complexity. Taken together, this study suggests that the number of RBPs with multiple RRMs has expanded in mammals and that the multiple sibling RRMs may recognize similar target motifs in a cooperative manner.     

miR‐938 promotes cell proliferation by regulating RBM5 in lung adenocarcinoma cells

A growing body of research suggests that microRNAs (miRNAs) may play a key part in the progression of various cancers, including lung adenocarcinoma (LUAD). However, the expression and mechanism of miR‐938 (microRNA‐938) in LUAD have not been defined. Compared with adjacent tissues, the level of miR‐938 was up‐regulated in LUAD tissues. miR‐938 expression was significantly associated with tumor size. In vitro assays indicated that miR‐938 expression was also increased in the LUAD cell lines. Overexpression of miR‐938 promoted LUAD cell proliferation, whereas down‐regulation of miR‐938 had the opposite effect. We identified RNA‐binding protein 5 (RBM5) as a potential target gene of miR‐938 in LUAD. Expression of RBM5 was down‐regulated in LUAD tumor tissues and negatively correlated with expression of miR‐938. Up‐regulation of RBM5 reversed cell proliferation by inhibition of miR‐938 expression in LUAD cells. These results showed that miR‐938 may act as an oncogenic miRNA by targeting RBM5 in LUAD, indicating that miR‐938 could be used as a potential therapeutic target for LUAD patients.     

1H, 13C and 15N resonance assignment of the first N-terminal RNA recognition motif (RRM) of the human heterogeneous nuclear ribonucleoprotein H (hnRNP H)

Human heterogeneous nuclear ribonucleoprotein H (hnRNP H) regulates alternative splicing of HIV-1 Tat pre-mRNA. The structure of the first N-terminal domain (residues 1–104) of hnRNP H was solved and its binding to an exonic splicing silencer (pESS2) studied. For this, all backbone and 85% of side-chain resonance frequencies were assigned.     

Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif

The essential pre-mRNA splicing factor, U2 auxiliary factor 65KD (U2AF(65)) recognizes the polypyrimidine tract (Py-tract) consensus sequence of the pre-mRNA using two RNA recognition motifs (RRMs), the most prevalent class of eukaryotic RNA-binding domain. The Py-tracts of higher eukaryotic pre-mRNAs are often interrupted with purines, yet U2AF(65) must identify these degenerate Py-tracts for accurate pre-mRNA splicing. Previously, the structure of a U2AF(65) variant in complex with poly(U) RNA suggested that rearrangement of flexible side-chains or bound water molecules may contribute to degenerate Py-tract recognition by U2AF(65). Here, the X-ray structure of the N-terminal RRM domain of U2AF(65) (RRM1) is described at 1.47 A resolution in the absence of RNA. Notably, RNA-binding by U2AF(65) selectively stabilizes pre-existing alternative conformations of three side-chains located at the RNA interface (Arg150, Lys225, and Arg227). Additionally, a flexible loop connecting the beta2/beta3 strands undergoes a conformational change to interact with the RNA. These pre-existing alternative conformations may contribute to the ability of U2AF(65) to recognize a variety of Py-tract sequences. This rare, high-resolution view of an important member of the RRM class of RNA-binding domains highlights the role of alternative side-chain conformations in RNA recognition.     

RBM10 inhibits cell proliferation of lung adenocarcinoma via RAP1/AKT/CREB signalling pathway

Initial functional studies have demonstrated that RNA‐binding motif protein 10 (RBM10) can promote apoptosis and suppress cell proliferation; however, the results of several studies suggest a tumour‐promoting role for RBM10. Herein, we assessed the involvement of RBM10 in lung adenocarcinoma cell proliferation and explored the potential molecular mechanism. We found that, both in vitro and in vivo, RBM10 overexpression suppresses lung adenocarcinoma cell proliferation, while its knockdown enhances cell proliferation. Using complementary DNA microarray analysis, we previously found that RBM10 overexpression induces significant down‐regulation of RAP1A expression. In this study, we have confirmed that RBM10 decreases the activation of RAP1 and found that EPAC stimulation and inhibition can abolish the effects of RBM10 knockdown and overexpression, respectively, and regulate cell growth. This effect of RBM10 on proliferation was independent of the MAPK/ERK and P38/MAPK signalling pathways. We found that RBM10 reduces the phosphorylation of CREB via the AKT signalling pathway, suggesting that RBM10 exhibits its effect on lung adenocarcinoma cell proliferation via the RAP1/AKT/CREB signalling pathway.     

RBPMS不同剪接体的真核表达和亚细胞定位

目的：构建具有多种剪接形式的RNA结合蛋白（RBPMS）基因的真核表达载体,并在真核细胞中表达,确定不同形式的RBPMS在细胞中的定位。方法：采用PCR技术从人卵巢cDNA文库中扩增RBPMS基因的几种完整编码序列（命名为RBPl～RBP4）,克隆到带绿色荧光蛋白标签的pEGFP-C1表达载体上,转染人胚肾细胞293T,Western印迹鉴定RBPMS的表达,并利用激光共聚焦显微镜观察RBPMS不同剪接体在细胞中的定位。结果：限制性内切酶分析和DNA序列测定表明构建的重组表达载体正确,Western印迹实验证明RBP1～RBP4表达成功。通过激光共聚焦显微镜观察,RBP1／4围绕胞核在核膜的周围呈聚集状分布;RBP2则在细胞质和细胞核中均有分布,但会出现斑点状聚集;RBP3呈半月状紧密分布在细胞核周围;RBPMS中的RNA识别基序缺失后,这种现象消失,与空载体对照类似,在细胞核和细胞质中均有分布。结论：构建并表达了RBPMS基因的真核表达载体,RBPMS不同剪接体及RNA识别基序缺失后具有不同的亚细胞分布模式,提示具有不同的功能。     

The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core

DEAD box family helicases consist of a helicase core that is formed by two flexibly linked RecA-like domains. The helicase activity can be regulated by N- or C-terminal extensions flanking the core. Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) is the first DEAD box helicase that forms a dimer using a unique dimerization domain. In addition to the dimerization domain, Hera contains a C-terminal RNA binding domain (RBD) that shares sequence homology only to uncharacterized proteins of the Deinococcus/Thermus group. The crystal structure of Hera_RBD reveals the fold of an altered RNA recognition motif (RRM) with limited structural homology to the RBD of the DEAD box helicase YxiN from Bacillus subtilis. Comparison with RRM/RNA complexes shows that a RNA binding mode different than that suggested for YxiN, but similar to U1A, can be inferred for Hera. The orientation of the RBD relative to the helicase core was defined in a second crystal structure of a Hera fragment including the C-terminal RecA domain, the dimerization domain, and the RBD. The structures allow construction of a model for the entire Hera helicase dimer. A likely binding surface for large RNA substrates that spans both RecA-like domains and the RBD is identified.     

A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities

An important group of splicing factors involved in constitutive and alternative splicing contain an arginine/serine (RS)-rich domain. We have previously demonstrated the existence of such factors in plants and report now on a new family of splicing factors (termed the RSZ family) from Arabidopsis thaliana which additionally harbor a Zn knuckle motif similar to the human splicing factor 9G8. Although only around 20 kDa in size, members of this family possess a multi-domain structure. In addition to the N-terminal RNA recognition motif (RRM), a Zn finger motif of the CCHC-type is inserted in an RGG-rich region; all three motifs are known to contribute to RNA binding. The C-terminal domain has a characteristic repeated structure which is very arginine-rich and centered around an SP dipeptide. One member of this family, atRSZp22, has been shown to be a phosphoprotein with properties similar to SR proteins. Furthermore, atRSZp22 was able to complement efficiently splicing deficient mammalian S100 as well as h9G8-depleted extracts. RNA binding assays to selected RNA sequences indicate an RNA binding specificity similar to the human splicing factors 9G8 and SRp20. Taken together, these result show that atRSZp22 is a true plant splicing factor which combines structural and functional features of both h9G8 and hSRp20.     

Novel CalphaNN structural motif for protein recognition of phosphate ions

Phosphate is one of the most frequently exploited chemical moieties in nature, present in a wide range of naturally occurring and critically important small molecules. Several phosphate group recognition motifs have been found for a few narrow groups of proteins, but for many protein families and folds the mode of phosphate recognition remains unclear. Here, we have analyzed the structures of all fold-representative protein-ligand complexes listed in the FSSP database, regardless of whether the bound ligand included a phosphate group. Based on a phosphate-binding motif that we identified in pyridoxal phosphate binding proteins, we have identified a new anion-binding structural motif, CalphaNN, common to 104 fold-representative protein structures that belong to 62 different folds, of which 86% of the fold-representative structures (51 folds) bind phosphate or lone sulfate ions. This motif leads to a precise mode for phosphate group recognition forming a structure where atoms of the phosphate group occupy the most favorable stabilizing positions. The anion-binding CalphaNN motif is based only on main-chain atoms from three adjacent residues, has a conservative betaalphaalpha or betaalphabeta geometry, and recognizes the free phosphate (sulfate) ion as well as one or more phosphate groups in nucleotides and in a variety of cofactors. Moreover, the CalphaNN motif is positioned in functionally important regions of protein structures and often residues of the motif directly participate in the function of the protein.     

Antizyme1基因转染对K562细胞增殖与凋亡的影响

研究鸟氨酸脱羧酶抗酶蛋白对人红白血病K562细胞增殖、三氧化二砷（ As2O3）诱导凋亡时的影响。方法: 定点突变技术构建缺失frameshift位点的pEGFP-N1-AZ1-mutation重组表达载体。脂质体法转染K562细胞,通过G418筛选获得稳定表达antizyme1的K562pAZ1m细胞系。采用不同浓度的As2O3处理细胞,通过MTT法检测细胞增殖,流式细胞术分析细胞周期及凋亡变化。并通过RT-PCR方法检测antiyme1转染对cyclin D1和survivin基因表达的影响。结果：获得稳定表达antizyme1的K562-AZ1m细胞株后,其增殖能力明显减慢。CyclinD1基因表达降低,细胞主要停滞于G0/G1期。在 As2O3的诱导作用下,细胞凋亡增多,survivin基因表达降低。结论：AZ1基因能够抑制K562细胞增殖,通过对cyclinD1的负调控使细胞周期停滞于G0/G1期。并可能通过下调survivin表达来加强 As2O3对其的诱导凋亡作用     

RBM5 and p53 expression after rat spinal cord injury: Implications for neuronal apoptosis

RBM5 (RNA-binding motif protein 5), a nuclear RNA binding protein, is known to trigger apoptosis and induce cell cycle arrest by regulating the activity of the tumor suppressor protein p53. However, its expression and function in spinal cord injury (SCI) are still unknown. To investigate whether RBM5 is involved in central nervous system injury and repair, we performed an acute SCI model in adult rats in this study. Our results showed RBM5 was unregulated significantly after SCI, which was accompanied with an increase in the levels of apoptotic proteins such as p53, Bax, and active caspase-3. Immunofluorescent labeling also showed that traumatic SCI induced RBM5 location changes and co-localization with active caspase-3 in neurons. To further probe the role of RBM5, a neuronal cell line PC12 was employed to establish an apoptotic model. Knockdown of RBM5 apparently decreased the level of p53 as well as active caspase-3, demonstrating its pro-apoptotic role in neurons by regulating expressions of p53 and caspase-3. Taken together, our findings indicate that RBM5 promotes neuronal apoptosis through modulating p53 signaling pathway following SCI.     

Two novel RNA binding proteins from Trypanosoma brucei are associated with 5S rRNA.

We have previously reported the identification of two closely related RNA binding proteins from Trypanosoma brucei which we have termed p34 and p37. The predicted primary structures of the two proteins are highly homologous with one major difference, an 18-amino-acid insert in the N-terminal region of p37. These two proteins have been localized to the nucleus based on immunofluorescence microscopy. To gain insight into their function, we have utilized UV crosslinking, coimmunoprecipitation, and sucrose density gradients to identify T. brucei RNA species that associate with p34 and p37. These experiments have demonstrated a specific interaction of both p34 and p37 with the 5S ribosomal RNA and indicate that other RNA species are unlikely to be specifically bound. This suggests a role for p34 and p37 in the import and/or assembly pathway of T. brucei 5S rRNA in ribosome biogenesis.     

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.     

Structure of the central RNA recognition motif of human TIA-1 at 1.95A resolution

T-cell-restricted intracellular antigen-1 (TIA-1) regulates alternative pre-mRNA splicing in the nucleus, and mRNA translation in the cytoplasm, by recognizing uridine-rich sequences of RNAs. As a step towards understanding RNA recognition by this regulatory factor, the X-ray structure of the central RNA recognition motif (RRM2) of human TIA-1 is presented at 1.95 Å resolution. Comparison with structurally homologous RRM-RNA complexes identifies residues at the RNA interfaces that are conserved in TIA-1-RRM2. The versatile capability of RNP motifs to interact with either proteins or RNA is reinforced by symmetry-related protein-protein interactions mediated by the RNP motifs of TIA-1-RRM2. Importantly, the TIA-1-RRM2 structure reveals the locations of mutations responsible for inhibiting nuclear import. In contrast with previous assumptions, the mutated residues are buried within the hydrophobic interior of the domain, where they would be likely to destabilize the RRM fold rather than directly inhibit RNA binding.     

冷应激条件下猪睾丸细胞中RNA结合基序蛋白3过表达对Caspase 3表达的影响

目的：探讨冷应激（32℃）条件下,猪睾丸（ST）细胞系中RNA结合基序蛋白3（RBM3）过表达时凋亡蛋白半胱天冬酶3（Caspase 3）表达量变化情况。方法：利用本实验室成功构建的携带绿色荧光蛋白（GFP）的RBM3过表达慢病毒载体pLenti6/V5-GW/EmGFP-RBM3和空病毒载体pLenti6/V5-GW/EmGFP-DEST分别感染ST细胞,作为过表达病毒（OEV）组和空载体病毒（EVV）组,此外还设立野生型细胞（WTC）组作对照,利用实时荧光定量RCR（qPCR）法和Western blot分析法检测各组中RBM3 mRNA和蛋白的表达情况。然后对各组细胞进行37℃以及32℃（2 h、4 h,8 h）的冷应激处理,利用酶联免疫吸附实验（ELISA）法检测各组Caspase 3表达量的变化。结果：OEV组RBM3基因和蛋白相对表达量高于EVV组和WTC组。在37℃以及32℃冷应激实验（2 h、4 h,8 h）中,OEV组Caspase 3表达量显著低于EVV组和WTC组。结论：冷应激ST细胞中RBM3过表达能够显著地降低Caspase 3的表达程度,为RBM3基因具有抵抗低温诱导ST细胞凋亡作用提供实验依据。     

中药组方黄芩汤抑制胃癌细胞增殖的实验研究

目的探讨黄芩汤对胃癌细胞生长增殖及干细胞标志物表达的影响。 方法采用体外优化培养的胃癌细胞株SGC-7901模型,分别加入生理盐水、5-FU、黄岑汤和5-FU+黄芪汤干预,MTT法检测胃癌细胞增殖情况,Real-time PCR检测胃癌干细胞相关表面标志物CD44、EpCAM、CD90的表达情况;并进一步利用胃癌细胞裸鼠荷瘤模型,观察黄岑汤协同5-FU对体内肿瘤生长的抑制效果。细胞增殖曲线多组间数据比较采用重复测量数据方差分析,单时间点多组数据采用单因素方差分析,组间比较采用Tukey法。 结果优化培养的胃癌细胞SGC- 7901呈球形生长,细胞活性染色显示良好的活性状态;MTT结果显示,黄岑汤组（0.44±0.04）能够抑制胃癌细胞的增殖,从第4天起与对照组（0.59±0.02）相比,差异具有统计学意义（F = 39.550,P < 0.01）;黄岑汤联合5-FU组（0.36±0.04）加强5-FU对肿瘤细胞的抑制作用,从第3天起与对照组（0.50±0.01）相比,差异具有统计学意义（F = 10.670,P < 0.01）,与5-FU组（0.42±0.03）对比,差异具有统计学意义（F = 10.670,P < 0.05）;Real-time PCR结果显示黄岑汤联合5-FU可抑制胃癌细胞中肿瘤干细胞相关表面标志物CD44、EpCAM、CD90表达（P < 0.01）;移植瘤生长抑制实验发现黄芪汤组对荷瘤鼠移植瘤的生长具有抑制作用,与对照组相比移植瘤体积减小,差异具有统计学意义（P < 0.01）,黄岑汤联合5-FU组与5-FU组相比对移植瘤抑制效果更明显,差异具有统计学意义（P < 0.01）。 结论黄芪汤能抑制胃癌细胞的生长和增殖,并能协同5-FU产生抗肿瘤作用。