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Identification and Bioinformatics Analysis of SnRK2 and cipk Family Genes in Sorghum

Agricultural Sciences in China 2010年第1期9卷 19-30页

作者： LI Li-bin ZHANG Yi-rong LIU Kai-chang NI Zhong-fu FANG Zhi-jun SUN Qi-xin GAO Jian-wei Vegetable Research Institute Shandong Academy of Agricultural Sciences Jinan 250100 P.R.China Department of Plant Genetics & Breeding China Agricultural University/National Center of Maize Improvement Beijing 100193 P.R. China Department of Scientific Research Administration Shandong Academy of Agricultural Sciences Jinan 250100 P.R.China Department of Plant Genetics & Breeding China Agricultural University/State Key Laboratory for Agrobiotechnology Beijing 100193 P.R. China Experimental Farm Shandong Academy of Agricultural Sciences Jinan 250100 P.R. China

Through bioinformatic data mining, 10 SnRK2 and 31 cipk genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the cipk genes have a few （no intron or less than 3 introns） or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and cipk genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and cipk into five parts. More than half SnRK2 and cipk genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the cipk family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of cipks is 61.66%. What＇s more, regarding to the sorghum SnRK2 and cipk kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum cipk genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and cipk genes may play important roles in stress response, growth and development.

关键词： Sorghum biocolor SnRK2 cipk phylogeny protein motif

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Functions and mechanisms of the CBL-cipk signaling system in plant response to abiotic stress

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Progress in Natural Science:Materials International 2009年第6期19卷 667-676页

作者： Ruifen Li a,1, Junwen Zhang a,b,1, Jianhua Wei a, Hongzhi Wanga, Yanzhen Wanga, Rongcai Ma a, a Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China b Life Science College, Capital Normal University, Beijing 100037, China [a]Beijing Agro-Biotechnology Research Center Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 China [b]Life Science College Capital Normal University Beijing 100037 China

To cope with environmental stimuli, plants have evolved precise regulatory mechanisms to perceive, transduce and respond to abiotic stresses that can negatively affect growth and development. The CBL-cipk signaling system is a newly emerging plant-specific and Ca2+-dependent network mediating abiotic stress tolerance. CBLs may sense a Ca2+ signature triggered by abiotic stresses, and have specific interactions with novel cipk-type kinases after binding Ca2+. The CBL/cipk complexes may post-translationally phosphory-late downstream target proteins to regulate abiotic stress tolerance in a cell or tissue-specific manner. In some cases transcription factors are induced to activate stress-responsive genes that control adaptation reactions. The CBL-cipk signaling system exhibits specificity, diversity and complexity. Meanwhile, cross talk also exists in the CBL-cipk signaling. To date, significant progress has been made in the role of the CBL-cipk signaling system in responding to salt, low K+ and to high pH, which will provide a fast and efficient method of molecular design breeding combined with the CBL/cipk engineering of crop plants, for enhanced tolerance to abiotic stresses. However, more CBL/cipk components remain to be identified, particularly from specific plants that grow in conditions with abiotic stress, and the specificity of their abiotic stress signaling will need to be dissected.

关键词： Calcium signal CBL cipk Signal transduction Abiotic stress

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Calcineurin-B-Like Protein CBL9 Interacts with Target Kinase cipk3 in the Regulation of ABA Response in Seed Germination

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Molecular Plant 2008年第2期1卷 238-248页

作者： Girdhar K. Pandey John J. Grant Yong Hwa Cheong Beom-Gi Kim Le Gong Li Sheng Luan Department of Plant and Microbial Biology University of California Berkeley CA 94720 USA Department of Plant Molecular Biology University of Delhi South Campus Benito Juarez Road New Delhi-110021 India Present address: Department of Bio-Environmental Science Sunchon National University Suncheon Jeonnam 540-742 Korea Present address: Department of Molecular Physiology and Biochemistry National institute of Agricultural Biotechnology Suwon 441-707 Korea

Calcium plays a vital role as a second messenger in many signaling pathways in plants. The calcineurin B-like proteins （CBLs） represent a family of plant calcium-binding proteins that function in calcium signaling by interacting with their interacting protein kinases （cipks）. In our previous study, we have reported a role for one of the CBLs （CBL9） and one of the cipks （cipk3） in ABA signaling. Here, we have shown that CBL9 and cipk3 physically and functionally interact with each other in regulating the ABA responses. The CBL9 and cipk3 proteins interacted with each other in the yeast two- hybrid system and when expressed in plant cells. The double mutant cbl9cipk3 showed the similar hypersensitive response to ABA as observed in single mutants （cbl9 or cipk3）. The constitutively active form of cipk3 genetically complemented the cbl9 mutant, indicating that cipk3 function downstream of CBL9. Based on these findings, we conclude that CBL9 and cipk3 act together in the same pathway for regulating ABA responses.

关键词： ABA calcium CBL cipk osmotic stress signal transduction.

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欧洲葡萄中cipk基因的克隆及表达分析

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园艺学报 2017年第8期44卷 1463-1476页

作者：闫朝辉李桂荣扈岩松周瑞金扈惠灵苗卫东朱自果河南科技学院园艺园林学院河南新乡453003

以欧洲葡萄‘佳丽酿’(Carinena)为材料,利用RT-PCR方法获得两个cipk基因的全长cDNA序列,分别为Vvcipk13和Vvcipk14。Vvcipk13全长为1 501 bp,包括一个1 395 bp的ORF,编码465个氨基酸;Vvcipk14全长为1 616 bp,包括一个1 404 bp的ORF,编码468个氨基酸。生物信息学分析表明两个蛋白均含有两个保守结构域:丝氨酸/苏氨酸激酶结构域和NAF结构域,两个结构域之间有连接域,但Vvcipk13和Vvcipk14的同源性较低,仅有40.33%。利用荧光定量PCR技术研究Vvcipk13和Vvcipk14在葡萄不同组织、植物生长调节剂诱导和逆境胁迫下的表达模式,结果表明:Vvcipk13和Vvcipk14表达具有组织特异性,均在卷须中高表达;Vvcipk13对6-BA诱导有响应,而Vvcipk14对6-BA、ABA、IAA、SA、MeJA和GA_3等诱导均有不同程度的响应;Vvcipk13和Vvcipk14均响应高盐和干旱,但不响应低温,其中Vvcipk14的响应最为强烈。推测Vvcipk13和Vvcipk14在葡萄的非生物胁迫过程中发挥重要的作用。

关键词：葡萄 cipk 基因表达非生物逆境

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A Flower Specific Calcineurin B-Like Molecule (CBL)-Interacting Protein Kinase (cipk) Homolog in Tomato Cultivar Micro-Tom (<i>Solanum lycopersicum</i>L.)

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American Journal of Plant Sciences 2012年第6期3卷 753-763页

作者： Takashi Yuasa Yushi Ishibashi Mari Iwaya-Inoue Department of Bioresource Science Faculty of Agriculture Kyushu University Fukuoka Japan.

Floral and reproductive organs of higher plants are relatively sensitive to biotic and abiotic stresses compared with the vegetative organs. Calcineurin B-like molecule (CBL) interacting protein kinase (cipk) has appeared to be involved in acquired tolerance and acclimation under environmental stresses such as salinity, drought and chilling. Semi-quantitative RT-PCR using the vegetative and reproductive organs of tomato Micro-Tom (Solanum lycopersicum L.) at the various developmental stages indicated that Slcipk2 was expressed specifically in the floral organ. An anti-cipk specific antibody recognized the recombinant Slcipk2 specifically and cross-reacted to a cipk-related polypeptide at a significant level in flower, particularly in stamen. The flower specific cipk was tightly associated with the microsomes. In vitro pull-down assay of the recombinant Slcipk2 showed that Slcipk2 interacts with SlCBLs and stress-responsive transcription factors, SlERF7, SlCBF1 and SlAREB1. The present data suggested that the flower-specific cipk, Slcipk2, was involved in calcium signaling in tomato via CBLs and stress tolerance possibly mediated by the stress-responsive transcription factors in stamen.

关键词： Calcium CBL cipk Flower SnRK Tomato

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芍药cipk基因克隆及其响应钙调控的表达水平研究

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植物生理学报 2018年第8期54卷 1316-1324页

作者：汤寓涵夏星陈德伟赵大球陶俊扬州大学动物科学与技术学院江苏扬州225009 扬州大学园艺与植物保护学院江苏扬州225009

研究钙离子传感器cipk(calcineurin B-like protein-interacting protein kinase)基因在芍药(Paeonia lactiflora)不同组织及在正反向钙处理后花茎中的表达变化,为通过采前喷施钙溶液调控芍药花茎挺直度提供理论依据。本文实验以芍药‘... 详细信息

研究钙离子传感器cipk(calcineurin B-like protein-interacting protein kinase)基因在芍药(Paeonia lactiflora)不同组织及在正反向钙处理后花茎中的表达变化,为通过采前喷施钙溶液调控芍药花茎挺直度提供理论依据。本文实验以芍药‘红艳争辉’花茎RNA为模板,采用PCR技术对芍药cipk基因进行克隆,并通过定量实时PCR技术对Pl cipk基因表达进行分析。结果显示,克隆获得的Pl cipk基因(Gea Bank MH748106)长1 467 bp,具有由1 314个碱基组成的完整开放阅读框,共编码438个氨基酸。Pl cipk基因在N端具有一个蛋白激酶催化域,在C端具有一个高度保守的NAF调控域,属于cipk家族基因。Pl cipk基因在芍药各组织中均有表达,但在花茎中表达最高;在芍药花茎中,Pl cipk基因的表达随着生长发育逐渐增加;采前钙处理提高了芍药花茎中Pl cipk基因的表达,而钙螯合剂处理降低了其表达,推测钙能够调控芍药花茎中Pl cipk基因的表达,影响其强度。本研究从一定程度上说明钙处理使钙调磷酸酶B蛋白(CBL)-cipk调控增强,花茎品质提高,也为应用钙提高芍药切花花茎挺直度提供一定的理论参考。

关键词：芍药 cipk 克隆表达分析钙调控

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New insights into the evolution and functional divergence of the cipk gene family in Saccharum

New insights into the evolution and functional divergence of...

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2019年中国作物学会学术年会

作者：苏炜华 Yongjuan Ren Dongjiao Wang Long Huang Hui Ling Yachun Su Ning Huang Hanchen Tang Liping Xu Youxiong Que Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Key Laboratory of Genetics Breeding and Multiple Utilization of Crops Ministry of Education College of Crop Science Fujian Agriculture and Forestry University

【Research background】 CBL-interacting protein kinases(cipks) are the primary components of calcium sensors and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Sugarcane is an important sugar crop that contributes up to about 80% of the world sugar production. To date, cipk genes have not been investigated in sugarcane. 【Materials and methods】 In this study, sequence and evolution analysis of the Sscipk genes were conducted using the available sugarcane genome data. In addition, the expression patterns of the cipk gene family in the presence of abscisic acid(ABA), polyethylene glycol(PEG), and sodium chloride(NaCl) were detected by qRT-PCR. The allogenic expression of Sccipks and interactions between Sccipks and ScCBLs were also explored. Under salinity stress, the growth status of E. coli cells expressing Sccipks was analyzed. Furthermore, their subcellular localization, a bimolecular fluorescence complementation assay(BiFC), and transient overexpression in Nicotiana benthamiana were also investigated.【Result and analysis】 In this study, 48 cipk genes(Ss cipks) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the Sscipk gene family may have undergone six gene duplication events from the last common ancestor(LCA) of Ss cipks. The gene structure of Ss cipks also incurred substantial variations during evolution, with the number of introns varying from 0 to 15. Whole-genome duplications(WGDs) and signal-gene replications served as the driving force for the amplification of Sscipks. Ten Sc cipk genes were amplified from sugarcane(Saccharum spp. hybrids). Expression analyses of Sccipk genes using qRT-PCR revealed that Sccipks are differentially expressed in response to ABA, PEG, and NaCl. Subcellular localization of Sccipks revealed that the fusion protein of four Sccipk::GFP were all expressed in the cytoplasm and plasma membrane, except for

关键词： sugarcane cipk gene evolution biotic and abiotic stresses transient overexpression protein interaction

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植物中CBL-cipk途径转导特异Ca^(2+)信号的分子机制

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植物遗传资源学报 2010年第4期11卷 462-468,473页

作者：张成伟王天宇黎裕中国农业科学院作物科学研究所北京100081

Ca2+作为植物中普遍存在的第二信使,其信号传感器CBL(calcineurin B-like protein)及与CBL互作的蛋白cipk(CBL-interacting protein kinase)所构成的CBL-cipk信号转导途径在转导特异Ca2+信号过程中起重要的作用。由于植物同时受多种复... 详细信息

Ca2+作为植物中普遍存在的第二信使,其信号传感器CBL(calcineurin B-like protein)及与CBL互作的蛋白cipk(CBL-interacting protein kinase)所构成的CBL-cipk信号转导途径在转导特异Ca2+信号过程中起重要的作用。由于植物同时受多种复杂环境因素影响,因此必须同时对各种复杂因素作出响应并转导并存的信号。CBL和cipk在结构、表达以及功能上的特异性构成了CBL-cipk途径能够转导特异Ca2+信号的分子基础。本文在介绍CBL、cipk的基础上,着重对其组合成的CBL-cipk途径转导特异Ca2+信号的分子机制进行综述。

关键词： CBL cipk Ca2+信号

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乌拉尔甘草cipk基因家族鉴定与表达分析

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生物学杂志 2022年第1期39卷 62-68页

作者：仙亚杰王斐谢双全陈喜凤沈海涛李鸿彬石河子大学生命科学学院新疆植物药资源利用教育部重点实验室石河子832003

为挖掘乌拉尔甘草钙调磷酸酶B互作蛋白激酶(Calcineurin B like protein interacting protein kinase,cipk)家族成员特征并预测其功能,利用生物信息学方法鉴定乌拉尔甘草cipk家族基因,并对其进行系统发育、基因结构、保守结构域及进化... 详细信息

为挖掘乌拉尔甘草钙调磷酸酶B互作蛋白激酶(Calcineurin B like protein interacting protein kinase,cipk)家族成员特征并预测其功能,利用生物信息学方法鉴定乌拉尔甘草cipk家族基因,并对其进行系统发育、基因结构、保守结构域及进化关系、表达特征等分析。从乌拉尔甘草基因组中鉴定获得22个Gucipk基因,分布于19个不同的染色体位置;氨基酸序列比对分析发现多数Gucipk都含有1个Ser/Thr结构域、1个NAF结构域以及PPI结构域;进化树分析结果显示,22个Gucipk基因可分为5个亚组。Gucipk基因的上游启动子中存在一些非生物胁迫和激素应答元件,推测Gucipk基因的功能发挥可能受不同信号的调控。根据组织特异性表达特征可将Gucipk分为Ⅰ~Ⅳ4个组,其中Ⅱ组中6个Gucipk成员在根、茎和叶片中的表达量较高,Ⅰ、Ⅲ、Ⅳ组的Gucipk成员在根、茎、叶组织中的表达相对较低。利用qRT-PCR分析Gucipk响应不同非生物胁迫的表达特征,结果表明:在盐、氧化、干旱、高温和低温胁迫下,Gucipk基因受到不同胁迫的诱导表达。结果为进一步探究Gucipk的功能和可能的调控机制提供了一定参考。

关键词：乌拉尔甘草 cipk 基因家族鉴定基因表达分析非生物胁迫

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水稻cipk基因家族的鉴定及Oscipk5受稻瘟病菌诱导的qRT-PCR分析

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福建农业学报 2019年第11期34卷 1237-1245页

作者：喻丝丝罗曦连玲许惠滨陈丽萍魏毅东蔡秋华谢华安张建福福建农林大学农学院福建福州350002 福建省农业科学院水稻研究所福建福州350019 闽台作物有害生物生态防控国家重点实验室/农业部华南杂交水稻种质创新与分子育种重点实验室/福州(国家)水稻改良分中心/福建省作物种质创新与分子育种省部共建国家重点实验室培育基地/杂交水稻国家重点实验室华南研究基地/福建省作物分子育种工程实验室/福建省水稻分子育种重点实验室/水稻国家工程实验室福建福州350003

【目的】植物通过启动一系列信号传导过程来应对外部环境,这些过程通常涉及多种蛋白激酶,包括钙调神经磷酸酶B样蛋白互作激酶(calcineurin B-like protein-interacting protein kinases, cipks)。为更加清晰全面地了解水稻cipk基因家族... 详细信息

【目的】植物通过启动一系列信号传导过程来应对外部环境,这些过程通常涉及多种蛋白激酶,包括钙调神经磷酸酶B样蛋白互作激酶(calcineurin B-like protein-interacting protein kinases, cipks)。为更加清晰全面地了解水稻cipk基因家族,本研究根据最新的基因组测序数据对水稻基因组中的cipks进行了鉴定。【方法】通过探讨拟南芥和水稻中cipks蛋白家族的结构特点,结合生物信息学和qRT-PCR技术系统分析水稻中cipks家族蛋白的结构。结合转录组数据,比较了粳稻云引受稻瘟病菌诱导后的表达情况。【结果】根据最新的水稻基因组数据,鉴定出31个水稻Oscipk基因。系统发育树分析结果表明,31个Oscipk基因可分为5个亚家族,这些亚家族具有不同的外显子-内含子和UTR的结构特点。从广谱抗稻瘟病品种粳稻云引受稻瘟病菌诱导的基因表达谱的趋势聚类中筛选出了Oscipk5基因并对其进行了表达分析,结果表明,云引中Oscipk5基因受稻瘟病菌的诱导表达。【结论】内含子缺失和片段重复在水稻Oscipk基因家族的扩展中起到重要作用,同时Oscipk5受到稻瘟病菌的诱导表达。

关键词：水稻 cipk 基因家族 Oscipk5 稻瘟病菌 qRT-PCR

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