基因选择性剪接的生物信息学研究概况

基因选择性剪接现象是真核生物基本而又重要的调控机制。由于基因的选择性剪接在形成生物复杂性和多样性上具有极其重要的作用,同时选择性剪接与许多人类疾病也密切相关。因此,研究基因选择性剪接是一项十分重要的工作。生物信息学作为一门新兴的学科在研究基因选择性剪接上起关键的作用,尤其在研究基因表达调控机制、选择性剪接基因预测以及选择性剪接基因进化上。本文综述了这方面的最新研究进展,为更深入了解真核生物基因的表达调控机理提供依据。     

植物基因选择性剪接: 断舍离合, 达权知变

选择性剪接是基因转录后的mRNA通过不同的剪接方式产生多样性成熟转录本的过程, 是真核生物细胞中一种重要的转录后调控方式。植物基因也常通过这种断舍离合的方式产生一专多能的转录本, 达到调节多种生命活动的目的。相较于动物, 植物中该领域的研究起步较晚, 但近年来也取得了长足的进步。该文综述了植物基因选择性剪接的生物学意义、剪接方式和机制、研究方法以及在生长发育与环境胁迫适应性调节中的作用, 并展望了未来的研究方向。     

可变剪接在植物免疫中的研究进展

可变剪接是生物重要的转录后修饰过程,是转录组和蛋白组多样性的重要来源.可变剪接参与了植物众多生理过程,包括植物昼夜节律、生长发育等,在植物响应生物和非生物胁迫过程中尤为普遍.近年来,可变剪接被认为是植物抵御病原菌侵染的重要调控机制.本文综述了可变剪接在植物免疫各个层面的调控作用,包括调节重要免疫受体、R基因、激素信号路...     

寻找mRNA的选择性剪接

在真核生物的基因中,mRNA选择性剪接现象十分普遍。mRNA选择性剪接导致一个基因多转录本的产生,被认为是高等生物增加蛋白质多样性的主要机制,且已发现与许多人类疾病密切相关。发现这些转录本的选择性剪接位点、新的外显子和外显子组合,乃至获得这些剪接变异体的完整克隆,对于基因功能的深入研究十分必要。简要介绍了几种在mRNA水平探索选择性剪接的方法。     

mRNA前体选择性剪接的研究进展

mRNA前体的选择性剪接（又称可变剪／拼接）是真核生物的一种基本而又重要的调控机制,它精细协调基因的功能,高效调节基因的定量表达以及蛋白功能的多样化,影响主要发育方向的决定,对细胞的分化、发育、生理功能和病理状态都有重要意义。选择性剪接与许多人类疾病密切相关。目前在生物信息学领域已有选择性剪接数据库的构建,用于选择性剪接的信息存储和处理。     

植物丝氨酸/精氨酸丰富(SR)蛋白的结构和功能及其在植物发育中的作用

丝氨酸／精氨酸丰富（SR）蛋白家族是真核生物中的一类剪接因子,在前体mRNA的组成性和选择性剪接中起作用。本文就近十几年来SR蛋白结构和功能及其在植物发育中的作用的研究进展作以介绍。     

植物干旱胁迫信号转导及其调控机制研究进展

干旱是严重限制作物生长及产量的环境因子之一。经过长期的进化,植物形成了一套响应干旱胁迫的信号转导机制,包括对干旱胁迫信号的感知,第二信使的产生,信号转导和信号网络的形成。信号转导的结果是导致相关基因的表达和蛋白的合成,进而引起植物体渗透调节及抗氧化系统的改变,最终使植物适应干旱逆境或增强植物抗旱能力。干旱胁迫通常会促进ROS的积累及其他次级信号分子的产生。MAPK级联途径是真核生物信号转导最为保守的途径,在植物的生长发育及各种胁迫信号的传导中均起着较重要的作用。综述干旱胁迫信号及ROS→MAPK和ROS→Ca2+介导的信号途径,以及信号转导途径的调控机制。     

Pre-mRNA选择性剪接的调控及选择性剪接数据库

Pre-mRNA选择性剪接是真核生物转录组和蛋白质组多样性的主要来源,也是细胞分化、发育等过程中重要的基因表达调控方式。约95%的人类多外显子基因存在RNA选择性剪接|很多人类基因疾病的发生与RNA剪接错误相关。随着共转录现象的发现,RNA选择性剪接调控机制研究也取得了很大进展。本文分别从序列层面和核小体定位、组蛋白修饰、DNA甲基化及非编码RNA等表观遗传层面,系统地阐述了RNA选择性剪接的调控机制。为便于搜索,本文介绍了近10年来RNA选择性剪接相关的数据库。     

表观遗传调控pre-mRNA的选择性剪接

选择性剪接是真核生物基因表达过程中的关键环节,是蛋白质多样性的主要来源,在生物的分化、发育及疾病的发生中扮演重要角色。传统的选择性剪接调控机制的研究多集中于RNA序列元件及与之相关的一些剪接因子,但近期的突破性研究指出表观遗传因素在选择性剪接的调控中发挥重要作用。DNA甲基化、染色质结构、组蛋白修饰相互影响并作用于pre-mRNA的选择性剪接,构成一个庞大、复杂的调控网络,表明表观遗传因素不仅决定着基因转录的起始,还影响其转录本剪接的结果。文章综述了近年来pre-mRNA选择性剪接的表观遗传调控的研究进展,探讨了DNA甲基化、染色质结构、组蛋白修饰在pre-mRNA选择性剪接中的可能作用,并展望了其对人类疾病研究所带来的深远影响。     

水稻NBS-LRR基因选择性剪接的全基因组检测及分析

选择性剪接是促进基因组复杂性和蛋白质组多样性的一种主要机制,但是对水稻NBS-LRR序列选择性剪接的全基因组分析却未见报道。通过隐马尔柯夫模型搜索,从TIGR数据库里得到了855条编码NBS-LRR基序的序列。利用这些序列在KOME、TIGR基因索引及UniProt三个数据库中进行同源搜索,获得同源的完整cDNA序列、假设一致性序列和蛋白质序列。再利用Spidey和SIM4程序把完整cDNA序列和假设一致性序列联配到相应的BAC序列上来预测选择性剪接。蛋白质序列和基因组序列之间的联配使用tBLASTn。在这875个NBS-LRR基因中,119个基因具有选择性剪接现象,其中包括71内含子保留,20个外显子跳跃,25个选择性起始,16个选择性终止,12个5′端的选择性剪接和16个3′端选择性剪接。大多数选择性剪接都为两个和多个转录本所支持。可以通过访问http://www.bioinfor.org查询这些数据。进而通过生物信息学分析剪接边界发现外显子跳跃和内含子保留的‘GT…AG’的规则不如组成型的保守。这暗示了它们是通过不同的调控机制来指导剪接变构体的形成。通过分析内含子保留对蛋白质的影响,发现选择性剪接的蛋白更倾向于改变其C端氨基酸序列。最后对选择性剪接的组织分布和蛋白质定位进行分析,结果表明选择性剪接的最大类的组织分布是根和愈伤组织。超过1/3剪接变构体的蛋白质定位是质膜和细胞质。这些选择性剪接蛋白可能在抗病信号转导中起到重要作用。     

MAPK级联途径调控植物细胞胞质分裂

胞质分裂(cytokinesis)是细胞分裂的最后关键一步,产生2个含有完整的遗传物质和胞质细胞器的子细胞．植物胞质分裂包括细胞板的形成,这一过程是在成膜体的牵引下由一些植物特有的步骤完成的．促分裂原活化蛋白激酶(MAPK)级联途径在真核生物中是高度保守的,由MAPKs,MAPKKs,MAPKKKs组成,通过MAPKKK→ MAPKK → MAPK的逐级磷酸化传递细胞信号．近来的研究表明, NACK-MAPKKK→MAPKK→MAPK→MAP65构成的信号途径调控植物细胞的胞质分裂．本文就这一信号途径,总结了植物胞质分裂机制的研究进展,并对其中的问题进行了讨论与展望．     

Signal convergence through the lenses of MAP kinases: paradigms of stress and hormone signaling in plants

Common mechanisms plants use to translate the external stimuli into cellular responses are the activation of mitogen-activated protein kinase (MAPK) cascade. These MAPK cascades are highly conserved in eukaryotes and consist of three subsequently acting protein kinases, MAP kinase kinase kinase (MAPKKK), MAP kinase kinase (MAPKK) and MAP kinase (MAPK) which are linked in various ways with upstream receptors and downstream targets. Plant MAPK cascades regulate numerous processes, including various environmental stresses, hormones, cell division and developmental processes. The number of MAPKKs in Arabidopsis and rice is almost half the number of MAPKs pointing important role of MAPKKs in integrating signals from several MAPKKKs and transducing signals to various MAPKs. The cross talks between different signal transduction pathways are concentrated at the level of MAPKK in the MAPK cascade. Here we discussed the insights into MAPKK mediated response to environmental stresses and in plant growth and development.     

OMTK1, a novel MAPKKK, channels oxidative stress signaling through direct MAPK interaction

In common with other eukaryotes, plants utilize mitogen-activated protein kinase (MAPK) cascades to mediate responses to a wide variety of stimuli. In contrast to other eukaryotes, plants have an unusually large number of MAPK components, such as more than 20 MAPKs, 10 MAPK kinases (MAPKKs), and 60 MAPKK kinases (MAPKKKs) in Arabidopsis (MAPK Group (2002) Trends Plant Sci. 7, 301-308). Presently it is mostly unknown how MAPK signaling specificity is generated in plants. Here we have isolated OMTK1 (oxidative stress-activated MAP triple-kinase 1), a novel MAPKKK from alfalfa (Medicago sativa). In plant protoplasts, OMTK1 showed basal kinase activity and was found to induce cell death. Among a panel of hormones and stresses tested, only H(2)O(2) was found to activate OMTK1. Out of four MAPKs, OMTK1 specifically activated MMK3 resulting in an increased cell death rate. Pull-down analysis between recombinant proteins indicated that OMTK1 directly interacts with MMK3 and that OMTK1 and MMK3 are part of a protein complex in vivo. These results indicate that OMTK1 plays a MAPK scaffolding role and functions in activation of H(2)O(2) -induced cell death in plants.     

The c-Jun N-terminal protein kinase family of mitogen-activated protein kinases (JNK MAPKs)

The c-Jun N-terminal protein kinase mitogen-activated protein kinases (JNK MAPKs) are an evolutionarily-conserved family of serine/threonine protein kinases. First identified in 1990 when intraperitoneal injection of the protein synthesis inhibitor cycloheximide activated a 54 kDa protein kinase, the JNK MAPKs have now taken on a prominent role in signal transduction. This research has revealed a number of levels of complexity. Alternative gene splicing is now recognised to result in ten different JNK MAPK isoforms of 46-55 kDa, and these isoforms differ in their substrate affinities. Furthermore, although originally classified as stress-activated protein kinases (SAPKs), or SAPKs, the JNK MAPKs are also critical mediators of signal transduction in response to stimulation by cytokines and some growth factors. JNK MAPKs have been shown to be critical mediators in dorsal closure in developing Drosophila embryos, and targeted knockout of murine JNK MAPKs has suggested a critical involvement of these kinases in mammalian embryonic development. Recent work has also highlighted their importance in programmed cell death. Thus, the JNK MAPKs may provide a critical target for regulation in both normal and diseased states.     

<Emphasis Type="Italic">Toxoplasma gondii</Emphasis> Expresses Two Mitogen-Activated Protein Kinase Genes That Represent Distinct Protozoan Subfamilies

All eukaryotes express mitogen-activated protein kinases (MAPKs) that govern diverse cellular processes including proliferation, differentiation, and survival. Even though these proteins are highly conserved throughout nature, MAPKs from closely related species often possess distinct signature sequences, making them well suited as drug discovery targets. Based on the central amino acid in the TXY dual phosphorylation loop, mammalian MAPKs are classified as extracellular signal-regulated kinases (ERKs), c-Jun amino-terminal kinases (JNKs), or p38 stress-response MAPKs. The presence of MAPKs in nonmetazoan eukaryotes suggests significant evolutionary conservation of these important signalling pathways. We recently cloned a novel stress-response MAPK gene (tgMAPK1) from Toxoplasma gondii, an obligate intracellular human parasite that can cause life-threatening infections in immunocompromised patients, and we now present data on a second T. gondii MAPK gene (tgMAPK2) that we cloned. We show that tgMAPK1 and tgMAPK2 are members of two distinct and previously unknown protozoan MAPK subfamilies that we have named pzMAPKl/pzMAPK3 and pzMAPK2. Our phylogenetic analysis of a collection of protozoan and metazoan MAPK genes in relation to ERK8-like genes demonstrates that an ERK8-like family, which includes the pzMAPK2 subfamily, is represented across a large variety of eukaryotic kingdoms and is evolutionarily very distant from other MAPK families.     

Mitogen-activated protein kinase cascades in plants: a new nomenclature

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules in eukaryotes, including yeasts, animals and plants. These protein phosphorylation cascades link extracellular stimuli to a wide range of cellular responses. In plants, MAPK cascades are involved in responses to various biotic and abiotic stresses, hormones, cell division and developmental processes. Completion of the Arabidopsis genome-sequencing project has revealed the existence of 20 MAPKs, 10 MAPK kinases and 60 MAPK kinase kinases. Here, we propose a simplified nomenclature for Arabidopsis MAPKs and MAPK kinases that might also serve as a basis for standard annotation of these gene families in all plants.     

Determination of primary sequence specificity of Arabidopsis MAPKs MPK3 and MPK6 leads to identification of new substrates

MAPKs (mitogen-activated protein kinases) are signalling components highly conserved among eukaryotes. Their diverse biological functions include cellular differentiation and responses to different extracellular stress stimuli. Although some substrates of MAPKs have been identified in plants, no information is available about whether amino acids in the primary sequence other than proline-directed phosphorylation (pS-P) contribute to kinase specificity towards substrates. In the present study, we used a random positional peptide library to search for consensus phosphorylation sequences for Arabidopsis MAPKs MPK3 and MPK6. These experiments indicated a preference towards the sequence L/P-P/X-S-P-R/K for both kinases. After bioinformatic processing, a number of novel candidate MAPK substrates were predicted and subsequently confirmed by in vitro kinase assays using bacterially expressed native Arabidopsis proteins as substrates. MPK3 and MPK6 phosphorylated all proteins tested more efficiently than did another MAPK, MPK4. These results indicate that the amino acid residues in the primary sequence surrounding the phosphorylation site of Arabidopsis MAPK substrates can contribute to MAPK specificity. Further characterization of one of these new substrates confirmed that At1g80180.1 was phosphorylated in planta in a MAPK-dependent manner. Phenotypic analyses of Arabidopsis expressing phosphorylation site mutant forms of At1g80180.1 showed clustered stomata and higher stomatal index in cotyledons expressing the phosphomimetic form of At1g80180.1, providing a link between this new MAPK substrate and the defined role for MPK3 and MPK6?in stomatal patterning.     

Creation of a stress-activated p90 ribosomal S6 kinase. The carboxyl-terminal tail of the MAPK-activated protein kinases dictates the signal transduction pathway in which they function

Mitogen-activated protein kinase-activated protein kinases (MAPKAPKs) lie immediately downstream of the mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK), and p38 MAPK. Although the family of MAPKAPKs shares sequence similarity, it demonstrates selectivity for the upstream activator. Here we demonstrate that each of the ERK- and p38 MAPK-regulated MAPKAPKs contains a MAPK docking site positioned distally to the residue(s) phosphorylated by MAPKs. The isolated MAPK docking sites show specificity for the upstream activator similar to that reported for the full-length proteins. Moreover, replacement of the ERK docking site of p90 ribosomal S6 kinase with the p38 MAPK docking site of MAPKAPK2 converts p90 ribosomal S6 kinase into a stress-activated kinase in vivo. It is apparent that mechanisms controlling events downstream of the proline-directed MAPKs involve specific MAPK docking sites within the carboxyl termini of the MAPKAPKs that determine the cascade in which the MAPKAPK functions.