CircRNA肿瘤相关生物学功能的研究进展

环状RNA(circRNA)是一类具有环状结构的非编码RNA(noncoding RNAs, ncRNA),广泛存在于多种生物细胞中,具有结构稳定、序列保守及细胞或组织特异性表达等特征。已被证实circRNA在许多癌症中存在表达异常,参与了恶性肿瘤的发生发展。CircRNA在细胞中的分布与其功能发挥密切相关。研究表明,胞核分布的circRNA可以参与调节mRNA转录和表观遗传调控,胞质分布的circRNA具有充当"miRNA海绵"、与RNA结合蛋白结合、影响蛋白质翻译、编码蛋白质等功能。本文对circ RNA在肿瘤中发挥的相关生物学功能进行综述,以期为后续研究提供一定的理论依据。     

环状RNA及其在神经退行性疾病中的作用

随着高通量测序技术的出现,对转录组进一步的研究已经成为可能。新兴转录本环状RNA(circular RNA, circRNA)是一种无5’端帽子和3’端poly (A)尾结构的内源性共价环形非编码RNA分子。在过去的十年间,人们逐渐发现circRNA在基因表达过程中发挥重要作用,激发了人们的研究兴趣。此篇文章我们较为系统地整理了circRNA的一般特性、生物发生、作用机制,并重点阐述了circRNA在神经退行性疾病中的重要作用,这将有助于寻找疾病相关新的生物标志物,为进一步探究此类疾病的预防、诊断及治疗方案提供新思路。     

环形RNA 在疾病中的研究进展

环形RNA(circular RNA circRNA)是由前体RNA的3'末端和5'末端首尾相连形成的环状非编码RNA,可竞争内源性RNA,调节基因的表达。环形RNA在发现之初,被认为是由于错误剪接产生的,未引起重视,随着RNA测序和生物信息等技术的发展大量的环形RNA被发现,并逐渐成为非编码RNA的研究热点。虽然目前对其功能了解甚少,但已有的研究表明环形RNA可以对基因转录后进行调控。本文将从环形RNA的发现过程、形成机制、生物学功能、与疾病的关系以及研究中存在的问题进行综述,有助于进一步研究中心法则,同时为疾病诊治提供新的方向。     

IRES介导的非帽依赖翻译调控研究进展

内部核糖体进入位点(Internal ribosome entry site, IRES)是一种存在于RNA内部的特殊功能元件,其可在不依赖5’端帽子结构的情况下直接招募核糖体启动蛋白翻译,已被发现与多种细胞过程密切相关。近来,越来越多的证据表明IRES在环形RNA翻译调控中扮演着极其重要的角色,由此IRES引起人们的极大关注。本文针对目前真核细胞中IRES介导的翻译调控机制进行了综述,并对IRES元件相关生物信息学工具进行了总结。     

长链非编码RNA与恶性肿瘤发生发展关系的研究进展

人类基因组数目庞大,其形成的基因调控网络控制着组织、器官细胞的增殖、分化和凋亡。但是,整个基因组中仅约2%的基因是编码RNA,可以翻译成蛋白质,98%左右的基因为非编码RNA。之前人们普遍认为非编码RNA不能翻译有效的蛋白质产生相应的功能,被视为基因组中的"废物"。目前,大量研究表明非编码RNA并不是基因组序列中没用的产物,而是未知的"黑暗物质",已有大量的研究发现非编码RNA在多种生物过程中起着重要的作用,并且在一些重大疾病如肿瘤、心血管的发生发展中发挥着不可小觑的作用。本文就长链非编码RNA在恶性肿瘤的发生发展中的作用机制做一综述。     

单增李斯特菌hfq基因的克隆及分子特征分析

目的:了解单增李斯特菌(Listeria monocytogenes,LM)SB5野毒株ncRNA伴侣分子hfq基因及其编码蛋白质的分子生物学特征。方法:利用PCR方法对hfq基因进行扩增、克隆及测序,对hfq基因分子特征进行分析,预测其编码蛋白质的二三级结构及功能活性位点,对其进行同源性及遗传变异分析。结果:LM hfq基因全长234 bp,编码77个氨基酸,对推导的Hfq氨基酸序列分析发现从N端到C端包含1个α-螺旋及5个β-折叠,具有RNA结合位点及六聚体结合位点。LM-SB5 hfq基因核苷酸序列与李斯特菌属各菌株同源率为94.5~100%,与其他种属细菌同源率为36.19~62.39%。结论:Hfq蛋白具有RNA的结合位点,可能在细菌ncRNA调节基因表达过程中发挥重要作用。     

十字花科植物种子低分子RNA提取方法比较

非编码RNA不翻译成蛋白质,它们通过转录、转录后及翻译水平调控靶基因表达,在植物生长发育及逆境胁迫中发挥功能。目前,大量种子萌发期特异表达的非编码RNA (Non-coding RNA)已被发现,高效提取种子低分子RNA是对其进行研究的关键。本研究将介绍一种改良SDS RNA提取方法,并与Trizol、CTAB法、RNA提取试剂盒进行比较。结果表明:这种方法可以高效提取用于Northern blotting、RT-PCR等分子生物学分析的十字花科植物种子低分子RNA。改良SDS RNA提取方法为种子非编码RNA研究、种子萌发生理及分子育种研究提供了帮助。     

长链非编码RNA及其与疾病相关性的研究进展*

人类基因组中,用于蛋白质编码的核酸序列约占1.5%,另外98.5%的非蛋白编码基因被视为"噪音"序列,并未引起人们的注意。随着测序技术的发展,人们发现大部分的基因被转录成RNA,其中多数为长度大于200nt且不编码蛋白质的长链非编码RNA(Long non-coding RNA, lncRNA),其作用机制包括支架分子、引导分子等,广泛参与细胞发育、增殖及迁移过程,且其水平的改变又与肿瘤、代谢性疾病等相关。本文主要对lncRNA的分类、作用机制及涉及的疾病等进行综述,为进一步研究lncRNA的功能机制奠定基础。     

环形RNA全长组装与定量工具的研究进展

环形RNA是一种广泛存在于真核细胞的内源性RNA,由前体RNA反向剪接而成,不具有5’末端帽子和3’末端poly(A)尾巴,呈封闭环状结构。环形RNA通过miRNA海绵结合等方式参与基因表达调控等许多重要的生物学过程。环形RNA可以通过可变剪接产生不同的环形RNA转录本,因此获取环形RNA转录本内部全长序列信息以及对环形RNA内部可变剪接产物进行精确定量是揭示环形RNA调控功能的前提。生物信息学工具能够高效便捷的处理高通量测序数据,被普遍用来鉴别和分析环形RNA。本文介绍了环形RNA的产生机制以及功能特性,对环形RNA检测、全长序列组装以及定量相关计算工具进行综述。     

环形RNA分子揭秘

环形RNA分子是一类不具有5'末端帽子和3'末端poly(A)尾巴、并以共价键形成环形结构的非编码RNA分子。利用针对环形结构RNA分子的实验和计算方法,并结合新一代高通量测序,现已在多种细胞内发现了大量环形RNA分子的稳定存在。目前,尽管环形RNA分子的产生机制及其代谢仍然不清楚,但是已有的研究表明环形RNA分子具有调控基因表达的功能。对环形RNA分子的产生机制和功能等的进一步研究,将为人们深入理解生命活动在转录水平的复杂性调控提供重要的分子基础和研究依据。     

Palytoxin Acts on Na+,K+-ATPase but not Nongastric H+,K+-ATPase

Palytoxin (PTX) opens a pathway for ions to pass through Na,K-ATPase. We investigate here whether PTX also acts on nongastric H,K-ATPases. The following combinations of cRNA were expressed in Xenopus laevis oocytes: Bufo marinus bladder H,K-ATPase α₂- and Na,K-ATPase β₂-subunits; Bufo Na,K-ATPase α₁- and Na,K-ATPase β₂-subunits; and Bufo Na,K-ATPase β₂-subunit alone. The response to PTX was measured after blocking endogenous Xenopus Na,K-ATPase with 10 μm ouabain. Functional expression was confirmed by measuring ⁸⁶Rb uptake. PTX (5 nm) produced a large increase of membrane conductance in oocytes expressing Bufo Na,K-ATPase, but no significant increase occurred in oocytes expressing Bufo H,K-ATPase or in those injected with Bufo β₂-subunit alone. Expression of the following combinations of cDNA was investigated in HeLa cells: rat colonic H,K-ATPase α₁-subunit and Na,K-ATPase β₁-subunit; rat Na,K-ATPase α₂-subunit and Na,K-ATPase β₂-subunit; and rat Na,K-ATPase β₁- or Na,K-ATPase β₂-subunit alone. Measurement of increases in ⁸⁶Rb uptake confirmed that both rat Na,K and H,K pumps were functional in HeLa cells expressing rat colonic HKα₁/NKβ₁ and NKα₂/NKβ₂. Whole-cell patch-clamp measurements in HeLa cells expressing rat colonic HKα₁/NKβ₁ exposed to 100 nm PTX showed no significant increase of membrane current, and there was no membrane conductance increase in HeLa cells transfected with rat NKβ₁- or rat NKβ₂-subunit alone. However, in HeLa cells expressing rat NKα₂/NKβ₂, outward current was observed after pump activation by 20 mm K⁺ and a large membrane conductance increase occurred after 100 nm PTX. We conclude that nongastric H,K-ATPases are not sensitive to PTX when expressed in these cells, whereas PTX does act on Na,K-ATPase.     

The sodium cycle: A novel type of bacterial energetics

The progress of bioenergetic studies on the role of Na⁺ in bacteria is reviewed. Experiments performed over the past decade on several bacterial species of quite different taxonomic positions show that Na⁺ can, under certain conditions, substitute for H⁺ as the coupling ion. Various primary Na⁺ pumps ( generators) are described, i.e., Na⁺-motive decarboxylases, NADH-quinone reductase, terminal oxidase, and ATPase. The formed is shown to be consumed by Na⁺ driven ATP-synthase, Na⁺ flagellar motor, numerous Na⁺, solute symporters, and the methanogenesis-linked reverse electron transfer system. InVibrio alginolyticus, it was found that , generated by NADH-quinone reductase, can be utilized to support all three types of membrane-linked work, i.e., chemical (ATP synthesis), osmotic (Na⁺, solute symports), and mechanical (rotation of the flagellum). InPropionigenum modestum, circulation of Na⁺ proved to be the only mechanism of energy coupling. In other species studied, the Na⁺ cycle seems to coexist with the H⁺ cycle. For instance, inV. alginolyticus the initial and terminal steps of the respiratory chain are Na⁺ - and H⁺-motive, respectively, whereas ATP hydrolysis is competent in the uphill transfer of Na⁺ as well as of H⁺. In the alkalo- and halotolerantBacillus FTU, there are H⁺ - and Na⁺-motive terminal oxidases. Sometimes, the Na⁺-translocating enzyme strongly differs from its H⁺-translocating homolog. So, the Na⁺-motive and H⁺-motive NADH-quinone reductases are composed of different subunits and prosthetic groups. The H⁺-motive and Na⁺-motive terminal oxidases differ in that the former is ofaa ₃-type and sensitive to micromolar cyanide whereas the latter is of another type and sensitive to millimolar cyanide. At the same time, both Na⁺ and H⁺ can be translocated by one and the sameP. modestum ATPase which is of the F₀F₁-type and sensitive to DCCD. The sodium cycle, i.e., a system composed of primary generator(s) and consumer(s), is already described in many species of marine aerobic and anaerobic eubacteria and archaebacteria belonging to the following genera:Vibrio, Bacillus, Alcaligenes, Alteromonas, Salmonella, Klebsiella, Propionigenum, Clostridium, Veilonella, Acidaminococcus, Streptococcus, Peptococcus, Exiguobacterium, Fusobacterium, Methanobacterium, Methanococcus, Methanosarcin, etc. Thus, the sodium world seems to occupy a rather extensive area in the biosphere.     

Role of the furosemide-sensitive Na+/K+ transport system in determining the steady-state Na+ and K+ content and volume of human erythrocytesin vitro andin vivo

Summary To study the physiological role of the bidirectionally operating, furosemide-sensitive Na⁺/K⁺ transport system of human erythrocytes, the effect of furosemide on red cell cation and hemoglobin content was determined in cells incubated for 24 hr with ouabain in 145mm NaCl media containing 0 to 10mm K⁺ or Rb⁺. In pure Na⁺ media, furosemide accelerated cell Na⁺ gain and retarded cellular K⁺ loss. External K⁺ (5mm) had an effect similar to furosemide and markedly reduced the action of the drug on cellular cation content. External Rb⁺ accelerated the Na⁺ gain like K⁺, but did not affect the K⁺ retention induced by furosemide. The data are interpreted to indicate that the furosemide-sensitive Na⁺/K⁺ transport system of human erythrocytes mediates an equimolar extrusion of Na⁺ and K⁺ in Na⁺ media (Na⁺/K⁺ cotransport), a 1:1 K⁺/K⁺ (K⁺/Rb⁺) and Na⁺/Na⁺ exchange progressively appearing upon increasing external K⁺ (Rb⁺) concentrations to 5mm. The effect of furosemide (or external K⁺/Rb⁺) on cation contents was associated with a prevention of the cell shrinkage seen in pure Na⁺ media, or with a cell swelling, indicating that the furosemide-sensitive Na⁺/K⁺ transport system is involved in the control of cell volume of human erythrocytes. The action of furosemide on cellular volume and cation content tended to disappear at 5mm external K⁺ or Rb⁺. Thein vivo red cell K⁺ content was negatively correlated to the rate of furosemide-sensitive K⁺ (Rb⁺) uptake, and a positive correlation was seen between mean cellular hemoglobin content and furosemide-sensitive transport activity. The transport system possibly functions as a K⁺ and waterextruding mechanism under physiological conditiosin vivo. The red cell Na⁺ content showed no correlation to the activity of the furosemide-sensitive transport system.     

Sodium ATPase and Sodium/proton Antiporter Are Not Obligatory for Sodium Homeostasis of Enterococcus hirae at Acid pH

Enterococcus hirae grows in a broad pH range from 5 to 11. An E. hirae mutant 7683 lacking the activities of two sodium pumps, Na⁺-ATPase and Na⁺/H⁺ antiporter, does not grow in high Na⁺ medium at pH above 7.5. We found that 7683 grew normally in high Na⁺ medium at pH 5.5. Although an energy-dependent sodium extrusion at pH 5.5 was missing, the intracellular levels of Na⁺ and K⁺ were normal in this mutant. The Na⁺ influx rates of 7683 and two other strains at pH 5.5 were much slower than those at pH 7.5. These results suggest that Na⁺ elimination of this bacterium at acid pH is achieved by a decrease in Na⁺ entry and a normal K⁺ uptake.     

Intracellular calcium content of human erythrocytes: Relation to sodium transport systems

Summary To study the possible role of intracellular Ca (Ca _i ) in controlling the activities of the Na⁺–K⁺ pump, the Na⁺–K⁺ cotransport and the Na⁺/Li⁺ exchange system of human erythrocytes, a method was developed to measure the amount of Ca embodied within the red cell. For complete removal of Ca associated with the outer aspect of the membrane, it proved to be essential to wash the cells in buffers containing less than 20nm Ca. Ca was extracted by HClO₄ in Teflon^® vessels boiled in acid to avoid Ca contaminations and quantitated by flameless atomic absorption. Ca _i of fresh human erythrocytes of apparently healthy donors ranged between 0.9 and 2.8 mol/liter cells. The mean value found in females was significantly higher than in males. The interindividual different Ca contents remained constant over periods of more than one year. Sixty to 90% of Ca _i could be removed by incubation of the cells with A23187 and EGTA. The activities of the Na⁺–K⁺ pump, of Na⁺–K⁺ cotransport and Na⁺/Li⁺ exchange and the mean cellular hemoglobin content fell with rising Ca _i ; the red cell Na⁺ and K⁺ contents rose with Ca _i . Ca depletion by A23187 plus EGTA as well as chelation of intracellular Ca²⁺ by quin-2 did not significantly enhance the transport rates. It is concluded that the large scatter of the values of Ca _i of normal human erythrocytes reported in the literature mainly results from a widely differing removal of Ca associated with the outer aspect of the membrane.     

Nigericin-induced Na+/H+ and K+/H+ exchange in synaptosomes: Effect on [3H]GABA release

The effect of the putative K⁺/H⁺ ionophore, nigericin on the internal Na⁺ concentration ([Na _i ]), the internal pH (pH _i ), the internal Ca²⁺ concentration ([Ca _i ]) and the baseline release of the neurotransmitter, GABA was investigated in Na⁺-binding benzofuran isophtalate acetoxymethyl ester (SBFIAM), 2′,7′-bis(carboxyethyl)-5(6) carboxyfluorescein acetoxymethyl ester (BCECF-AM), fura-2 and [³H]GABA loaded synaptosomes, respectively. In the presence of Na⁺ at a physiological concentration (147 mM), nigericin (0.5 μM) elevates [Na _i ] from 20 to 50 mM, increases thepH _i , 0.16 pH units, elevates four fold the [Ca _i ] at expense of external Ca²⁺ and markedly increases (more than five fold) the release of [³H]GABA. In the absence of a Na⁺ concentration gradient (i.e. when the external Na⁺ concentration equals the [Na _i ]), the same concentration (0.5 μM) of nigericin causes the opposite effect on thepH _i (acidifies the synaptosomal interior), does not modify the [Na _i ] and is practically unable to elevate the [Ca _i ] or to increase [³H]GABA release. Only with higher concentrations of nigericin than 0.5 μM the ionophore is able to elevate the [Ca _i ] and to increase the release of [³H]GABA under the conditions in which the net Na⁺ movements are eliminated. These results clearly show that under physiological conditions (147 mM external Na⁺) nigericin behaves as a Na⁺/H⁺ ionophore, and all its effects are triggered by the entrance of Na⁺ in exchange for H⁺ through the ionophore itself. Nigericin behaves as a K⁺/H⁺ ionophore in synaptosomes just when the net Na⁺ movements are eliminated (i.e. under conditions in which the external and the internal Na⁺ concentrations are equal). In summary care must be taken when using the putative K⁺/H⁺ ionophore nigericin as an experimental tool in synaptosomes, as under standard conditions (i.e. in the presence of high external Na⁺) nigericin behaves as a Na⁺/H⁺ ionophore.     

Functional Consequences of Various Leucine Mutations in the M3/M4 Loop of the Na<Superscript>+</Superscript>,K<Superscript>+</Superscript>-ATPase α-Subunit

Leucines were mutated within the sequence L³¹¹ILGYTWLE³¹⁹ of the extracellular loop flanking the third (M3) and fourth (M4) transmembrane segments (M3/M4 loop) of the Torpedo Na⁺,K⁺-ATPase α-subunit. Replacement of Leu³¹¹ with Glu resulted in a considerable loss of Na⁺,K⁺-ATPase activity. Replacement of Leu³¹³ with Glu shifted the equilibrium of E₁P and E₂P toward E₁P and reduced the rate of the E₁P to E₂P transition. The reduction of the transition rate and stronger inhibition of Na⁺,K⁺-ATPase activity by Na⁺ at higher concentrations together suggest that there is interference of Na⁺ release on the extracellular side in the Leu³¹³ mutant. Thus, Leu³¹³ could be in the pathway of Na⁺ exit. Replacement of Leu³¹⁸ with Glu yielded an enzyme with significantly reduced apparent affinity for both vanadate and K⁺, with an equilibrium shifted toward E₂P and no alteration in the transition rate. The reduced vanadate affinity is due to the lower rate of production of vanadate-reactive [K⁺ ₂]E₂ caused by inhibition of dephosphorylation through reduction of the K⁺ affinity of E₂P. Thus, Leu³¹⁸ may be a critical position in guiding external K⁺ to its binding site.