玉米D亚族bZIP转录因子基因的数据库挖掘、分析、克隆与表达

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杨艳歌, 吕维涛, 孙冬梅, 凌毅, 邓馨. 玉米D亚族bZIP转录因子基因的数据库挖掘、分析、克隆与表达. 作物学报, 2013, 39(12): 2115-2122[YANG Yan-Ge, LÜ Wei-Tao, SUN Dong-Mei, LING Yi, DENG Xin. Database Mining, Bioinformatics, Cloning, and Expression Analyses of D Subfamily bZIP Genes in Maize. Acta Agronomica Sinica, 2013, 39(12): 2115-2122] 复制到剪切板

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玉米D亚族bZIP转录因子基因的数据库挖掘、分析、克隆与表达

杨艳歌^1,², 吕维涛², 孙冬梅^1,^*, 凌毅^3,^*, 邓馨^2,^*

¹黑龙江八一农垦大学生命科学技术学院, 黑龙江大庆163319

²中国科学院植物研究所资源植物研发重点实验室, 北京100093

³中国农业大学生物学院, 北京100193

^* 通讯作者(Corresponding authors): 孙冬梅, E-mail:sdmlzw@126.com, Tel: 13089069957; 凌毅, E-mail:lingyi01@cau.edu.cn, Tel: 010- 62734385; 邓馨, E-mail:deng@ibcas.ac.cn, Tel: 010-62836261

收稿日期:2013-06-09

基金:本研究由国家转基因生物新品种培育科技重大专项(2011ZX08009-002)和黑龙江省研究生创新科研项目资金一般项目(YJSCX2012-26 1HLJ)资助。

摘要

碱性亮氨酸拉链(basic leucine zipper, bZIP)是真核生物特有的转录因子家族, 在高等植物基因表达与调控中起重要作用。本文通过对玉米基因组数据库中收录的全长cDNA序列全基因组范围的bZIP分析, 发现其中25个序列编码D亚族bZIP转录因子。针对这些序列进行生物信息学分析、染色体分布和直系同源组的分类分析, 发现部分序列可能是由同一基因座编码, 但不同方式剪切形成的。对部分基因克隆和测序发现了更多的剪切形式。定量检测其中3个基因在ABA和干旱胁迫条件下的表达发现, 其中1个受ABA诱导, 2个受ABA抑制, 但均不受干旱胁迫影响。表明玉米中D亚族基因可能参与ABA响应。

关键词: 玉米; bZIP转录因子; D亚族; 数据库挖掘; 基因表达

Database Mining, Bioinformatics, Cloning, and Expression Analyses of D Subfamily bZIP Genes in Maize

YANG Yan-Ge^1,², LÜ Wei-Tao², SUN Dong-Mei^1,^*, LING Yi^3,^*, DENG Xin^2,^*

¹College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China

²Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China

³College of Life Science, China Agricultural University, Beijing 100193, China

Abstract

Basic leucine zipper (bZIP) is unique transcription factor family among eukaryotes, playing important roles in gene expression and regulation in higher plants. Here we reported the finding of 25 full length cDNA sequences encoding D subfamily of bZIP factors in maize from a database mining on whole genome level. The analysis of bioinformatics, chromosome distribution and classification of Possible Groups of Orthologous (PoGO) suggested the existence of diverse alternative splicing in some of these genes, which was supported by the sequencing results of the cloned cDNAs. The expression pattern of three representative genes in response to ABA and drought stress were examined by quantitative RT-PCR, and the results revealed different regulations of ABA on the expression of these genes. Our results suggest that D subfamily of bZIP genes in maize might involve in ABA signal pathway.

Keyword: Maize; bZIP transcription factor; D subfamily; Database mining; Gene expression

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碱性亮氨酸拉链(basic region/leucine zipper motif, bZIP)类的转录因子普遍存在于动植物及微生物中, 参与ABA信号转导和各种环境胁迫的响应等, 是一类重要的转录因子^{[ 1]}。它由一个二聚体化作用的亮氨酸拉链区域和一个DNA结合的碱性结构域组成。亮氨酸拉链结构域的典型特征是每7氨基酸的第7位含有一个亮氨酸, 以及其他疏水残基位于第3和第4位。DNA结合区域是由大约20个氨基酸组成的碱性结构域, 用于识别并结合G-box等顺式作用元件^{[ 2]}。bZIP类转录因子在未结合DNA之前以未折叠的单体形式存在, 受到逆境胁迫后以二聚体的形式结合DNA, 识别核心序列为ACGT的顺式作用元件^{[ 3]}。Jakoby等^{[ 4]}根据碱性亮氨酸区域的同源性和其他保守结构域的特性, 将拟南芥基因组中所有的bZIP类转录因子分成A、B、C、D、E、F、G、H、I和S类10个亚族, 认为在同一亚族的bZIP转录因子往往有相似的功能。拟南芥中D亚族有10个成员^{[ 4]}, 水稻中有16个^{[ 5]}。目前对不同植物中D亚族bZIP转录因子的研究表明, 该亚族基因主要参与病害防御和生理生长, 还参与生长发育进程^{[ 4]}。Correa等^{[ 5]}进一步提出了直系同源组(Possible Groups of Orthologues, PoGO)的分类, 其中将植物D亚族bZIP又分为5个组, 即D1~D5。其中D2和D4组主要参与生长发育进程, 如拟南芥中AtbZIP46/ Perianthia控制植物器官数目^{[ 6]}, 玉米的 Liguleless2 ( lg2)定位叶和鞘的边界^{[ 7]}; D3和D5组主要在植物防卫反应过程中起正向和负向双重调控作用^{[ 5]}, 如拟南芥中TGA4/OBF4/AtbZIP57可能通过AtEBP与PR启动子上的乙烯应答元件相结合起抗病作用^{[ 8, 9]}, 而TGA类型的bZIP转录因子与响应水杨酸(salicylic acid, SA)的顺式元件相结合, 在SA信号途径中起负调控作用^{[ 10]}。此外, D3和D5组基因还参与茉莉酸(jasmonic acid, JA)信号转导以及生长激素和磷缺陷的响应等^{[ 11]}。D1类的基因功能目前尚不清楚。

对拟南芥D亚族bZIP转录因子的研究表明, 该亚族的氨基酸序列具有极高的同源性, 如TGA4和TGA1氨基酸相似性达92%, TGA5、TGA6和TGA2的相似性分别达92.8%和95.3%, TGA4和TGA5有53%的氨基酸相同^{[ 8, 12]}。玉米中分离出2个bZIP蛋白基因OBF3.1和OBF3.2, 其氨基酸相似度达95.8%^{[ 13]}。不同植物中的该类基因保守性也极高, 拟南芥TGA1和烟草TGA1a有63%氨基酸相同^{[ 14]}。

进化研究表明, D亚族的基因与A、G亚族可能有共同的祖先^{[ 5]}。但几乎所有A亚族的基因都参与ABA信号转导, 并耐受抗旱等多种非生物胁迫^{[ 4]}, 而D亚族是否参与ABA信号和干旱等非生物胁迫响应尚无报道。本文利用基因组数据挖掘方法分析玉米D亚族bZIP基因, 克隆并研究其在ABA和干旱胁迫条件下的表达, 为进一步阐明bZIP转录因子D亚族的功能提供基础。

1 材料与方法

1.1 玉米材料及处理

将玉米( Zea maysL .) B73自交系种子置于湿润纱布上, 28℃暗培养2 d后, 种植于搅拌均匀的花土和蛭石的小花盆中, 在28℃、12 h/12 h光周期条件培养。取三叶一心期的幼苗, 将根部浸没在 100 μmol L^-1 ABA中进行处理, 并以溶剂作为对照, 于0、2、6和12 h处理后取叶片。同时, 三叶一心期时开始停止浇水, 进行干旱处理, 用土壤水分探测仪测定土壤水分含量。水分饱和时土壤水分含量在40%~50%之间, 15%~20%为轻度干旱(feebly arid, FA), 10%左右为中度干旱(moderate drought, MD), 5%左右为重度干旱(serious drought, SD), 并以同期生长的正常浇水的玉米幼苗作为对照(control check, CK), 按各处理分别取样, 立即用液氮处理并置-70℃保存。

1.2 RNA提取及第一链cDNA的合成

用总RNA提取试剂盒(TRIzol Reagent, TaKaRa)提取样品的总RNA, 并用DNase I (TaKaRa)纯化。按照SuperScript III反转录酶(Invitrogen)说明书合成第一链cDNA, 作为基因扩增及荧光定量PCR(Real time quantitative PCR, qRT-PCR)的模板。

1.3 基因克隆

用特异引物和高保真的Phusion High-Fidelity DNA聚合酶(NEB)进行基因扩增, Touchdown程序反应程序为98℃ 30 s; 98℃ 10 s, 62℃ 20 s, 72℃ 45 s, 退火温度每隔一个循环降低1℃, 至49℃; 最后延伸72℃ 10 min。PCR产物经1%琼脂糖凝胶电泳检测, 回收目的条带。连接Gateway载体pENTR/ D-TOPO (Invitrogen), 转化大肠杆菌感受态TOP10, 经菌液PCR筛选阳性克隆, 测序验证。

1.4 qRT-PCR

采用Toyobo公司SYBR Green Master Mix进行qRT-PCR, 反应体系含cDNA 1 μL、7.5 μL 2×SYBR Green Master Mix、引物(10 pmol μL^-1)各0.3 μL、ddH₂O 5.9 μL。以玉米β-tubulin为内参, 反应程序为94℃ 30 s; 94℃ 5 s, 54℃ 30 s, 72℃ 20 s, 共40个循环。采用基因相对表达分析2^-∆∆Ct法分析基因相对表达量^{[ 15]}。

1.5 数据库挖掘与生物信息学分析

利用ZmGDB (http://www.plantgdb.org/ZmGDB/)和MaizeGDB (http://www.maizegdb.org/)数据库进行玉米bZIP基因全长cDNA和基因组序列搜索以及染色体位置和外显子-内含子结构分析。bZIP蛋白多重序列比对由ClustalX 1.83构建, 使用软件默认参数^{[ 16]}, 根据比较结果, 用Genedoc进行保守序列分析, 用MEGA4构建系统进化树^{[ 17]}。以上述玉米基因组数据库为依据, 应用MEME (http://meme.nbcr.net/meme/ cgi-bin/meme.cgi)软件进行保守结构域分析。

2 结果与分析

2.1 玉米D亚族bZIP基因序列分析

将ZmGDB和MaizeGDB基因组数据库中收录的可能编码bZIP转录因子的全长cDNA序列与拟南芥D亚族基因进行序列比对分析, 发现25个与拟南芥D亚族基因同源性比较高的玉米bZIP序列。对这

25个基因编码产物分析发现它们与拟南芥D亚族bZIP转录因子相似, 除了共有bZIP结构域外, 紧跟着bZIP基元还有3个保守的motif (图1)。其中第一个motif是DOG1 (Delay of Germination 1)保守结构域^{[ 18]}, 该结构域曾在一个种子休眠关键基因 DELAY OF GERMINATION 1 ( DOG1)中发现, 但具体功能未知。

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图1 玉米D亚族bZIP蛋白保守结构图及保守基元的序列logo左图为玉米D亚族bZIP蛋白的结构, 右图为由MEME工具自动生成的玉米D亚族bZIPs的保守基元的序列logo。Fig. 1 Structure and sequence logos of the conserved domains of D subfamily bZIP transcription factors in maizeConserved domain structure of maize D subfamily bZIP factors is in the left panel; the sequence logos of the conserved motifs revealed by MEME is in the right panel.

很多报道指出D亚族基因氨基酸相似度较高。通过序列比对, 发现25个D亚族bZIP转录因子两两之间的氨基酸序列相似度在55%~99%之间, 蛋白的亮氨酸拉链区的下游至C末端的氨基酸序列高度保守(图2)。然而, 蛋白的N末端氨基酸序列差异很大, 可能与这些蛋白的不同功能或调节性质相关。

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	图2 玉米和拟南芥D亚族bZIP转录因子的多重序列比对Fig. 2 Alignment of D subfamily bZIP transcription factors from maize and Arabidopsis.

2.2 玉米D亚族bZIP基因在基因组中的分布

在序列比对中发现一些玉米D亚族bZIP基因具有完全相同或高度相似的编码序列。为了解这些基因之间的关系, 分析了这25个cDNA所对应的染色体位置, 发现除了第1和第5染色体外, 它们分布于其他8条染色体, 第10染色体上最多, 有7个基因; 第4和第9染色体上最少, 只有1个基因; 其余的5条染色体各有2~4个(图3)。同时我们根据基因组序列和cDNA序列比对, 分析相应基因的内含子-外显子结构, 发现D亚族基因内含子较多, 在5~12个之间(图4)。

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	图3 玉米D亚族bZIP基因在染色体上的分布Fig. 3 Chromosome locations of bZIPgenes of D subfamily in maize

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图4 拟南芥和玉米D亚族bZIP蛋白进化树及玉米D亚族 bZIP基因外显子-内含子组织结构图蓝色框表示外显子, 直线表示内含子。绿色和红色箭头分别表示起始密码子和终止密码子。Fig. 4 Phylogenetic tree of D subfamily bZIP from maize and Arabidopsis and the exon-intron structures of maize bZIP genesBlue boxes indicate exons. Line between boxes indicate introns. Green and red arrows represent initiation and termination codons, respectively.

发现有6组基因具有完全相同或高度相似的编码序列, 并位于同一个染色体的同一个基因座上(表1), 分别为: (1)BT088188、BT061346、BT034282、BT060754与BT064430, (2)BT043436、BT039852与BT063898, (3)BT037374与BT042450, (4)BT088145与BT069355, (5)BT038664与TGA4, (6)BT035801、BT034456与OBF3.1。其中第一组基因都位于第10染色体的144 522 640~144 530 848之间, 位置很接近。进一步分析这些基因的内含子-外显子结构发现, BT060754、BT064430的内含子-外显子结构也一样, 仅5-UTR和3-UTR序列不同; 二者氨基酸序列与BT034282相似性达到100%, 但内含子-外显子结构不同; BT088188和BT061346内含子-外显子结构相同, 但与其他3个不同。表明这5个基因可能是同一基因座编码的不同剪切方式造成的不同转录本。BT088145和BT069355都位于第2染色体6 717 439~ 6724101之间, 仅前者比后者多出N端的27个氨基酸, 其他序列完全相同, 但二者的内含子外显子结构差异很大; 都位于第7染色体133 128 880~ 133 137 073之间的BT039852比BT043436和BT063898多了N端50个氨基酸和1个内含子; 都位于第3染色体187 322 690~1 887 336 485之间的BT034456、BT035801和OBF3.1的外显子内含子结构相同, 但后者5-UTR短。另外2组基因分别位于第8染色体120 135 342~120 139 090区段和第10染色体49 981 532~49 984 883区段, 组内基因内含子外显子结构完全一样, 仅5-UTR和3-UTR序列不同。表明这5组内的不同基因很可能是预测得到的多种可能的转录本, 也有可能是不同剪切方式造成的。

另外, 位于第8染色体上的OBF3.2与位于第3染色体上的OBF3.1、BT035801和BT034456有较高的同源性, 第3染色体上的lg2与第6染色体上的TGA6有较高的同源性, 表明玉米基因组中的bZIP基因可能发生过复制。

表1 玉米D亚族bZIP基因的PoGO分组和染色体分布 Table 1 PoGO group and chromosomal distribution of D subfamily bZIP genes in maize

2.3 玉米D亚族bZIP基因进化分析

为了解玉米D亚族bZIPs的进化特征, 对玉米和拟南芥的D亚族bZIP转录因子构建了进化树(图4)。结果表明, 这些转录因子在进化树上的分布符合Correa等的PoGO分组^{[ 5]}。其中, BT063898等3个基因座编码的5个bZIP序列与AtbZIP65构成D1组分支; 另外ZmTGA6等3个玉米bZIP因子与AtbZIP21组成D2分支; BT088188等3个基因座编码的8个bZIP序列组成一个小分支, 与AtbZIP22等4个拟南芥bZIP因子和玉米TGA4的小分支共同形成D3组分支; BT085145等2个基因座编码的3个玉米bZIP序列与AtbZIP46组成D4分支; OBF3.1等3个基因座编码的5个bZIP因子组成一小支, 与AtbZIP20等3个拟南芥基因组成的小分支共同组成D5组分支。表明拟南芥和玉米的5个组分别具有共同祖先, 但在2种植物中平行进化, 在玉米中大量复制进化形成多个拷贝, 而在拟南芥中除D3组外都维持较低的拷贝数。

2.4 玉米D亚族bZIP基因的克隆

对玉米D亚族5个PoGO组的代表性bZIP基因进行扩增和克隆测序。获得的5个基因扩增产物中D3组的BT034282和D5组的BT034456和BT036137基因序列与预测的完全相同, D5组BT035801测序结果比预测长63个核苷酸(编码21个氨基酸的序列), 即预测的第1个内含子存在于转录本中; 而D2组BT066129核酸序列与公布序列相比有8个碱基差异, 导致其中1个氨基酸不同。因基因克隆时选用高保真的DNA聚合酶进行扩增, 错配率非常低; 而且多个克隆测序发现此差异是所有克隆中共同存在的, 因此可以确定差异是真实存在的, 而不是PCR和克隆过程造成的。D5组的BT034456和BT035801存在于第10染色体的同一基因座, PCR与测序结果表明该基因确实存在不同剪切形式的转录本。上述结果表明这些基因在玉米幼苗中是转录的。然而D1组和D4组的基因没有得到扩增产物, 可能与这些基因在三叶一心期的幼苗中不表达, 或者表达水平低有关, 也可能是其所在区段的染色体结构特殊或GC含量较高所致。

2.5 玉米D亚族bZIP基因在ABA和干旱胁迫下的表达

由于BT034282可能是BT088188的不同剪切形式, BT036137与BT035801相似度极高, 无法获得特异性扩增, 故仅分析了D5组的BT036137、D3组的BT088188和D2组的BT066129这3个 bZIP基因应答ABA和干旱胁迫的表达谱。结果如图5所示, ABA处理后BT036137被诱导表达, 且表达量随着时间的延长有逐渐升高的趋势, 12 h可达到0 h的2倍以上; 而BT088188和BT066129的转录表达受ABA胁迫的抑制, 且12 h表达量最低(图5-A)。干旱处理后, 这3个基因的表达均受到抑制, 随着干旱的加强, 表达量逐渐降低, 甚至几乎不表达(图5-B)。

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	图5 玉米D亚族bZIP基因在ABA和干旱处理下的表达CK: 对照; FA: 轻度干旱; MD: 中度干旱; SD: 重度干旱。Fig. 5 Expression of D subfamily bZIPs in maize underABA and drought treatmentsCK, FA, MD, and SD indicate control check, feebly arid, moderate drought, and serious drought, respectively.

3 讨论

bZIP转录因子在ABA和植物逆境反应中扮演着重要角色, 干旱、高盐及其他逆境条件下, 植物细胞内源ABA含量迅速增加, 促使大量ABA诱导基因表达, bZIP转录因子可以与ABA诱导基因的启动子的ABRE(ABA-responsive element)结合来调节下游靶基因的表达^{[ 19]}。A亚族基因在ABA和胁迫下的表达和在逆境基因表达调控方面的功能已被证实, 其中代表性的基因包括 ABI5及 ABI5-like、 ABF1- ABF4和 AREB3等。D亚族是除A亚族外唯一具有44个氨基酸组成的bZIP domain的亚族, 与A亚族可能从共同的祖先进化而来^{[ 5]}。但对D亚族 bZIP基因的研究主要限于生物胁迫、植物发育以及参与JA和SA信号转导等^{[ 11]}, 对ABA和干旱等非生物胁迫的响应和所具有的功能尚无报道。

对拟南芥、水稻和毛果杨bZIPs基因的进化研究表明, bZIPs基因家族的祖先在单双子叶植物分化之前就已经存在^{[ 5]}。本研究通过对玉米bZIP转录因子的全长cDNA序列分析, 得到25个D亚族玉米bZIP基因; 进化树分析结果表明, 这25个玉米D亚族bZIP转录因子与拟南芥D亚族基因聚到一起, 推测玉米与拟南芥bZIP转录因子很可能存在共同的祖先。这25个玉米D亚族bZIP基因分布于第8条染色体上, 且有6组为同一基因座编码的基因, 另外两组基因高度同源但分布于不同染色体, 每组组内基因序列甚至内含子-外显子结构都完全一样, 猜测可能是一个基因座编码的不同剪切方式的转录本。这可能与玉米bZIPs基因在进化过程中经历了整个基因组复制事件、染色体区域内的大片段复制事件以及接下来的基因缺失、小范围内的复制、局部重排、转座子跳跃、染色体倒置等事件有关, 使玉米D亚族的基因呈一定程度的重复性和冗余性。这些都表明D亚族bZIP基因在植物中是高度保守的。对拟南芥和玉米家族的保守结构域分析发现, 除典型bZIP motif外, 所有D亚族bZIPs中都含有1个DOG1保守结构域, 该结构域曾在一个种子休眠关键基因 DELAY OF GERMINATION 1 ( DOG1)中发现, 但具体功能未知。DOG1是与种子休眠相关的关键基因, 其受ABA调控^{[ 18, 20]}。最新研究表明DOG1不仅影响萌发还影响开花时间, 进而影响植物整个生命过程和适应能力^{[ 21]}。外显子捕获、重排和融合是新基因产生的进化机制之一^{[ 22]}。该亚族基因是否通过进化获得DOG1 motif进而获得新功能, 有待进一步研究。

目前的研究表明D2和D4组主要参与生长发育进程, D3和D5组bZIP转录因子在植物防卫反应中起调控作用, 参与JA、SA信号转导以及生长激素的响应等^{[ 5]}, 本文报道ABA处理可诱导D5组BT036137表达, 而抑制D3组BT088188和D2组BT066129的表达, 表明玉米中D亚族基因也参与ABA响应, 但是调控方式不同, 也表明D亚族的基因尽管相似度极高, 但可能在ABA途径中的作用可能不同。

4 结论

得到25个D亚族玉米bZIP基因, 其序列存在较大的重复性和冗余性, 均含有1个DOG1保守基序, 暗示该亚族基因与种子休眠、开花时间等可能有一定的关系。该亚族中BT036137基因受ABA诱导表达, 表明其可能参与ABA信号转导。

The authors have declared that no competing interests exist.

作者已声明无竞争性利益关系。The authors have declared that no competing interests exist.

参考文献

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2005

8.987

0.0

. 2005, 17:3470-3488

AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis

Fujita Y , Fujita M , Satoh R , Maruyama K , Parvez M M , Seki M , Hiratsu K , Ohme-Takagi M , Shinozaki K , Yamaguchi-Shinozaki K

ABSCISIC ACID–RESPONSIVE ELEMENT BINDING PROTEIN1 (AREB1) (i.e., ABF2) is a basic domain/leucine zipper transcription factor that binds to the abscisic acid (ABA)–responsive element (ABRE) motif in the promoter region of ABA-inducible genes. Here, we show that expression of the intactAREB1 gene on its own is insufficient to lead to expression of downstream genes under normal growth conditions. To overcome the masked transactivation activity of AREB1, we created an activated form of AREB1 (AREB1ΔQT). AREB1ΔQT-overexpressing plants showed ABA hypersensitivity and enhanced drought tolerance, and eight genes with two or more ABRE motifs in the promoter regions in two groups were greatly upregulated: late embryogenesis abundant class genes and ABA- and drought stress–inducible regulatory genes. By contrast, anareb1 null mutant and a dominant loss-of-function mutant of AREB1 (AREB1:RD) with a repression domain exhibited ABA insensitivity. Furthermore, AREB1:RD plants displayed reduced survival under dehydration, and three of the eight greatly upregulated genes were downregulated, including genes for linker histone H1 and AAA ATPase, which govern gene expression and multiple cellular activities through protein folding, respectively. Thus, these data suggest that AREB1 regulates novel ABRE-dependent ABA signaling that enhances drought tolerance in vegetative tissues.

... 碱性亮氨酸拉链(basic region/leucine zipper motif, bZIP)类的转录因子普遍存在于动植物及微生物中, 参与ABA信号转导和各种环境胁迫的响应等, 是一类重要的转录因子^[1] ...

2001

3.579

0.0

. 2001, 268(22):5655-5666

Plant bZIP G-box binding factors.

Yann Sibéril,Pierre Doireau,Pascal Gantet

UPRES-EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, UFR des Sciences et Techniques, Laboratoire de Physiologie Végétale, Parc de Grandmont, France
^* P. Gantet, UPRES-EA2106 ‘Biomolécules et Biotechnologies Végétales’, UFR des Sciences et Techniques, Laboratoire de Physiologie Végétale, Parc de Grandmont, 37200 Tours, France, Fax:/Tel.: + 33 2 47 36 70 42, E-mail:gantet@univ-tours.fr

In this review we sum-up the knowledge about bZIP G-box binding factors (GBFs), which possess an N-terminal, proline-rich domain. The GBF has been one of the most extensively studied transcription factor family. Based on protein sequence homology with yeast and animal basic leucine-zipper (bZIP) transcription factors, bioinformatic studies have identified their main structural domains (proline-rich, basic and leucine-zipper), which have been further functionally characterized byin vitro andin vivo experiments. Recent reports have led to the discovery of other GBF-specific short amino-acid sequences that may take part in the regulation of gene expression by post-transcriptional modifications or interaction with other proteins such as bZIP enhancing factors or plant 14-3-3-like proteins. We identified a GBF region, called the ‘multifunctional mosaic region’, that may be implicated in cytoplasmic retention, translocation to the nucleus and regulation of transcription. We also identified many conserved protein motifs that suggest a modular structure for GBFs. At the whole plant level, GBFs have been shown to be involved in developmental and physiological processes in response to major cues such as light or hormones. Nevertheless, it remains difficult to assign a physiological role to a particular GBF protein modular structure. Finally, bringing together these different aspects of GBF studies we propose a model describing the puzzling transduction pathway involving GBFs from cytoplasmic events of signal transduction to the regulation of gene expression in the nucleus.

... DNA结合区域是由大约20个氨基酸组成的碱性结构域, 用于识别并结合G-box等顺式作用元件^[2] ...

2005

1.086

0.0

J Genet. 2005, 84(2):183-187 DOI:10.1007/BF02715844

Effect of copy number and spacing of the ACGT and GTcis elements on transient expression of minimal promoter in plants

Rajesh Mehrotra⁽¹⁾, Kanti Kiran⁽¹⁾, Chandra Prakash Chaturvedi⁽¹⁾, Suraiya Anjum Ansari⁽¹⁾, Niraj Lodhi⁽¹⁾, Samir Sawant⁽¹⁾, Rakesh Tuli⁽¹⁾

1.National Botanical Research Institute, Rana Pratap Marg, 226 001, Lucknow, India

1.National Botanical Research Institute Rana Pratap Marg 226 001 Lucknow India

... bZIP类转录因子在未结合DNA之前以未折叠的单体形式存在, 受到逆境胁迫后以二聚体的形式结合DNA, 识别核心序列为ACGT的顺式作用元件^[3] ...

2002

11.047

0.0

. 2002, 7:106-111

bZIP transcription factors in Arabidopsis

Jakoby M , Weisshaar B , Droge-Laser W , Vicente-Carbajosa J , Tiedemann J , Kroj T , Parcy F , Grp bR

In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development. TheArabidopsis genome sequence contains 75 distinct members of the bZIP family, of which

50 are not described in the literature. Using common domains, the AtbZIP family can be subdivided into ten groups. Here, we review the available data on bZIP functions in the context of subgroup membership and discuss the interacting proteins. This integration is essential for a complete functional characterization of bZIP transcription factors in plants, and to identify functional redundancies among AtbZIP factors.

... Jakoby等^[4]根据碱性亮氨酸区域的同源性和其他保守结构域的特性, 将拟南芥基因组中所有的bZIP类转录因子分成A、B、C、D、E、F、G、H、I和S类10个亚族, 认为在同一亚族的bZIP转录因子往往有相似的功能 ...

... 拟南芥中D亚族有10个成员^[4], 水稻中有16个^[5] ...

... 目前对不同植物中D亚族bZIP转录因子的研究表明, 该亚族基因主要参与病害防御和生理生长, 还参与生长发育进程^[4] ...

... 但几乎所有A亚族的基因都参与ABA信号转导, 并耐受抗旱等多种非生物胁迫^[4], 而D亚族是否参与ABA信号和干旱等非生物胁迫响应尚无报道 ...

2008

4.092

0.0

. 2008, 3:e2944-null

The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes

Correa L G , Riano-Pachon D M , Schrago C G , Mueller-Roeber B , Vincentz M

Background

Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms.

Methodology/Principal Findings

We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy.

Conclusions/Significance

Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.

... 拟南芥中D亚族有10个成员^[4], 水稻中有16个^[5] ...

... Correa等^[5]进一步提出了直系同源组(Possible Groups of Orthologues, PoGO)的分类, 其中将植物D亚族bZIP又分为5个组, 即D1~D5 ...

... D3和D5组主要在植物防卫反应过程中起正向和负向双重调控作用^[5], 如拟南芥中TGA4/OBF4/AtbZIP57可能通过AtEBP与PR启动子上的乙烯应答元件相结合起抗病作用^[8,9], 而TGA类型的bZIP转录因子与响应水杨酸(salicylic acid, SA)的顺式元件相结合, 在SA信号途径中起负调控作用^[10] ...

... 进化研究表明, D亚族的基因与A、G亚族可能有共同的祖先^[5] ...

... 结果表明, 这些转录因子在进化树上的分布符合Correa等的PoGO分组^[5] ...

... D亚族是除A亚族外唯一具有44个氨基酸组成的bZIP domain的亚族, 与A亚族可能从共同的祖先进化而来^[5] ...

... 对拟南芥、水稻和毛果杨bZIPs基因的进化研究表明, bZIPs基因家族的祖先在单双子叶植物分化之前就已经存在^[5] ...

... 目前的研究表明D2和D4组主要参与生长发育进程, D3和D5组bZIP转录因子在植物防卫反应中起调控作用, 参与JA、SA信号转导以及生长激素的响应等^[5], 本文报道ABA处理可诱导D5组BT036137表达, 而抑制D3组BT088188和D2组BT066129的表达, 表明玉米中D亚族基因也参与ABA响应, 但是调控方式不同, 也表明D亚族的基因尽管相似度极高, 但可能在ABA途径中的作用可能不同 ...

1999

11.659

0.0

... 其中D2和D4组主要参与生长发育进程, 如拟南芥中AtbZIP46/ Perianthia控制植物器官数目^[6], 玉米的Liguleless2 (lg2)定位叶和鞘的边界^[7] ...

1999

6.16

0.0

. 1999, 19(4):489-495

The liguleless2 gene of maize functions during the transition from the vegetative to the reproductive shoot apex

Justine Walsh,Michael Freeling^*

Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720, USA
^**For correspondence (fax +510 6424995; e-mailfreeling@nature.berkeley.edu).

During a maize plant’s (Zea mays) development, the shoot apical meristem (SAM) generates an apex that proceeds through different phases: juvenile vegetative, adult vegetative and reproductive. During each phase the structures produced are distinguishable from structures produced during the other phases. In this paper, we demonstrate that the LIGULELESS2 (LG2) function is required for an accurate vegetative to reproductive phase transition. The maize geneliguleless2 (lg2) has been shown to encode a basic-leucine zipper (bZIP) protein and to function in narrowing the region from which the ligule and auricle develop in a typical maize leaf. Here we show thatlg2 mutant plants can have reduced long tassel branches, extra vegetative leaves and extra husk leaves when compared to wild-type siblings. This indicates a role for thelg2 gene in the vegetative to reproductive phase transition of the shoot apex. We also discuss a potential role for thelg2 gene in general phase transition processes.

... 其中D2和D4组主要参与生长发育进程, 如拟南芥中AtbZIP46/ Perianthia控制植物器官数目^[6], 玉米的Liguleless2 (lg2)定位叶和鞘的边界^[7] ...

2004

3.538

0.0

. , :null-null

... 3%, TGA4和TGA5有53%的氨基酸相同^[8,12] ...

2000

4.431

0.0

2003

8.987

0.0

2013

4.431

0.0

... 此外, D3和D5组基因还参与茉莉酸(jasmonic acid, JA)信号转导以及生长激素和磷缺陷的响应等^[11] ...

... 但对D亚族bZIP基因的研究主要限于生物胁迫、植物发育以及参与JA和SA信号转导等^[11], 对ABA和干旱等非生物胁迫的响应和所具有的功能尚无报道 ...

1997

4.15

0.0

Plant Mol Biol. 1997, 34(3):403-415

DNA-binding properties, genomic organization and expression pattern of TGA6, a new member of the TGA family of bZIP transcription factors in Arabidopsis thaliana

Chengbin Xiang⁽¹⁾, Zhonghe Miao⁽¹⁾, Eric Lam⁽¹⁾

1.AgBiotech Center, Cook College, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08903, USA

The TGA genes encode a family of basic domain-leucine zipper (bZIP) transcription factors that are conserved in higher plants. We have continued to unravel the complexity of this gene family by using a polymerase chain reaction (PCR)-based approach. Taking advantage of the conserved amino acid sequence in the bZIP domain found in all members of this gene family, two degenerate oligonucleotides were synthesized based on the sequence of this region in order to amplify by PCR the analogous genomic fragments from the various TGA loci in Arabidopsis. This approach has led us to the finding of a new member of the TGA gene family, and subsequently the isolation of a gene designated as TGA6. Further characterization of the TGA6 locus confirmed our prediction that the gene structure of this family is remarkably conserved. Genomic Southern blot analysis revealed that TGA6 is a single-copy gene in Arabidopsis. Based on the genomic sequence information, gene-specific primers were synthesized for isolating the cDNA that corresponds to the coding region. Subsequently, the cDNA for TGA6 was cloned and sequenced. Gel mobility shift assays with in vitro translated TGA6 protein showed that TGA6 is more like TGA5 in terms of its in vitro DNA-binding properties. The expression of TGA6 in different tissues was estimated by using reverse transcriptase (RT)-PCR and further analyzed in transgenic Arabidopsis lines expressing a TGA6 promoter-GUS fusion. TGA6 promoter activity is found primarily in roots of young seedlings. As seedlings develop, TGA6 is expressed in aging cotyledons, mesophyll cells of hydathodes on leaf margins, vascular tissue and trichomes of senescing rosette leaves, but is very low in primary roots of mature plants. High levels of expression persist in young lateral roots and in regions of the primary root where lateral roots are emerging. In flowers, the activity is localized predominantly to mature pollen grains. The expression pattern of TGA6 reported here is strikingly similar to that of an Arabidopsis acidic chitinase gene. Possible biological significance of TGA6 in cellular defense against pathogens and abiotic stress is discussed.

... 3%, TGA4和TGA5有53%的氨基酸相同^[8,12] ...

1993

6.16

0.0

. 1993, 3(5):669-679

Isolation of a maize bZIP protein subfamily: candidates for the ocs-element transcription factor

Rhonda C. Foley¹,Carol Grossman²,Jeff G. Ellis²,Danny J. Llewellyn²,Elizabeth S. Dennis²,W. James Peacock²,Karam B. Singh^1,2,*

¹ Department of Biology, University of California Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90024, USA
² CSIRO, Division of Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
^* *For correspondence (fax + 1 3102063987).

Ocs-elements, a family of 20 bp DNA sequences, are components of a number of promoters active in plants. In the maize BMS cell line the dominant ocs-element binding activity is the ocs-element transcription factor complex called OTF. The isolation of cDNA clones from a BMS cDNA expression library for two bZIP (basic region-leucine zipper) proteins that bind the ocs-element sequence and are good candidates for forming at least part of OTF is described. The two ocs-element binding proteins, called OBF3.1 and OBF3.2, are closely related, with the OBF3.1 protein sharing 95.8% amino acid homology with part of the OBF3.2 protein although there were significant differences in the 3′ untranslated regions. Genomic Southern blot analysis revealed a small gene family with a minimum of two OBF3 loci mapping to chromosomes 3L 105 and 8L075. The OBF3.1 protein shared considerable homology with the wheat HBP1b protein (80% amino acid identity) and to a lesser extent with the tobacco TGA1a protein. OBF3.1 like HBP1b was able to bind well to the Hex sequence but poorly to G-box/ABRE sequences. Interestingly, OBF3.1 bound eightfold more efficiently to an ocs-element sequence than TGA1a, raising the possibility that OBF3.1 and TGA1a may be distinct members of an OBF3/TGA subfamily.

... 8%^[13] ...

1992

9.205

0.0

... 不同植物中的该类基因保守性也极高, 拟南芥TGA1和烟草TGA1a有63%氨基酸相同^[14] ...

2001

4.011

0.0

. 2001, 25(4):402â408-null

... 采用基因相对表达分析2^-∆∆Ct法分析基因相对表达量^[15] ...

2003

0.0

... 83构建, 使用软件默认参数^[16], 根据比较结果, 用Genedoc进行保守序列分析, 用MEGA4构建系统进化树^[17] ...

2004

5.202

0.0

... 83构建, 使用软件默认参数^[16], 根据比较结果, 用Genedoc进行保守序列分析, 用MEGA4构建系统进化树^[17] ...

2006

9.737

0.0

. 2006, 103:17042-17047

Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis

Bentsink L , Jowett J , Hanhart C J , Koornneef M

Genetic variation for seed dormancy in nature is a typical quantitative trait controlled by multiple loci on which environmental factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a major scientific challenge, which also has relevance for agriculture and ecology. In this study we describe the identification of theDELAY OF GERMINATION 1 (DOG1) gene previously identified as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated by a combination of positional cloning and mutant analysis and is absolutely required for the induction of seed dormancy.DOG1 is a member of a small gene family of unknown molecular function, with five members inArabidopsis. The functional natural allelic variation present inArabidopsis is caused by polymorphisms in the cis-regulatory region of theDOG1 gene and results in considerable expression differences between theDOG1 alleles of the accessions analyzed.

... 其中第一个motif是DOG1 (Delay of Germination 1)保守结构域^[18], 该结构域曾在一个种子休眠关键基因DELAY OF GERMINATION 1 (DOG1)中发现, 但具体功能未知 ...

... DOG1是与种子休眠相关的关键基因, 其受ABA调控^[18,20] ...

2010

6.16

0.0

. 2010, 61(4):672-685

AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation

Takuya Yoshida^1,2,Yasunari Fujita²,Hiroko Sayama¹,Satoshi Kidokoro^1,2,Kyonoshin Maruyama²,Junya Mizoi²,Kazuo Shinozaki³,Kazuko Yamaguchi-Shinozaki^1,2,*

¹ Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
² Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
³ RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
^* For correspondence (fax +81 29 838 6643; e-mailkazukoys@jircas.affrc.go.jp).

A myriad of drought stress-inducible genes have been reported, and many of these are activated by abscisic acid (ABA). In the promoter regions of such ABA-regulated genes, conservedcis-elements, designated ABA-responsive elements (ABREs), control gene expression via bZIP-type AREB/ABF transcription factors. Although all three members of the AREB/ABF subfamily, AREB1, AREB2, and ABF3, are upregulated by ABA and water stress, it remains unclear whether these are functional homologs. Here, we report that all three AREB/ABF transcription factors require ABA for full activation, can form hetero- or homodimers to functionin nuclei, and can interact with SRK2D/SnRK2.2, an SnRK2 protein kinase that was identified as a regulator of AREB1. Along with the tissue-specific expression patterns of these genes and the subcellular localization of their encoded proteins, these findings clearly indicate that AREB1, AREB2, and ABF3 have largely overlapping functions. To elucidate the role of these AREB/ABF transcription factors, we generated anareb1 areb2 abf3 triple mutant. Large-scale transcriptome analysis, which showed that stress-responsive gene expression is remarkably impaired in the triple mutant, revealed novel AREB/ABF downstream genes in response to water stress, including many LEA class and group-Ab PP2C genes and transcription factors. Theareb1 areb2 abf3 triple mutant is more resistant to ABA than are the other single and double mutants with respect to primary root growth, and it displays reduced drought tolerance. Thus, these results indicate that AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent gene expression for ABA signaling under conditions of water stress.

... 3 讨论bZIP转录因子在ABA和植物逆境反应中扮演着重要角色, 干旱、高盐及其他逆境条件下, 植物细胞内源ABA含量迅速增加, 促使大量ABA诱导基因表达, bZIP转录因子可以与ABA诱导基因的启动子的ABRE(ABA-responsive element)结合来调节下游靶基因的表达^[19] ...

2010

4.15

0.0

Plant Mol Biol. 2010, 73(1-2):67 - 87 DOI:10.1007/s11103-009-9583-x

Cross-species approaches to seed dormancy and germination: conservation and biodiversity of ABA-regulated mechanisms and the BrassicaceaeDOG1 genes

Kai Graeber(1) Ada Linkies(1) Kerstin Müller(1) Andrea Wunchova(23) Anita Rott(1) Gerhard Leubner-Metzger(1)

1.University of Freiburg Botany/Plant Physiology, Institute for Biology II, Faculty of Biology Sch?nzlestr. 1 79104 Freiburg Germany
2.Palacky University in Olomouc Department of Cell Biology and Genetics Slechtitelu 11 78371 Olomouc-Holice Czech Republic
3.Mendel University of Agriculture and Forestry in Brno Department of Botany and Plant Physiology Zemedelska 1 61300 Brno Czech Republic

Seed dormancy is genetically determined with substantial environmental influence mediated, at least in part, by the plant hormone abscisic acid (ABA). The ABA-related transcription factorABI3/VP1 (ABA INSENSITIVE3/VIVIPAROUS1) is widespread among green plants. Alternative splicing of its transcripts appears to be involved in regulating seed dormancy, but the role ofABI3/VP1 goes beyond seeds and dormancy. In contrast,DOG1 (DELAY OF GERMINATION 1), a major quantitative trait gene more specifically involved in seed dormancy, was so far only known fromArabidopsis thaliana (AtDOG1) and whether it also has roles during the germination of non-dormant seeds was not known. Seed germination ofLepidium sativum (‘garden cress’) is controlled by ABA and its antagonists gibberellins and ethylene and involves the production of apoplastic hydroxyl radicals. We found orthologs ofAtDOG1 in the Brassicaceae relativesL. sativum (LesaDOG1) andBrassica rapa (BrDOG1) and compared their gene structure and the sequences of their transcripts expressed in seeds. Tissue-specific analysis ofLesaDOG1 transcript levels inL. sativum seeds showed that they are degraded upon imbibition in the radicle and the micropylar endosperm. ABA inhibits germination in that it delays radicle protrusion and endosperm weakening and it increasedLesaDOG1 transcript levels during early germination due to enhanced transcription and/or inhibited degradation. A reduced decrease inLesaDOG1 transcript levels upon ABA treatment is evident in the late germination phase in both tissues. This temporal and ABA-related transcript expression pattern suggests a role forLesaDOG1 in the control of germination timing of non-dormantL. sativum seeds. The possible involvement of the ABA-related transcription factors ABI3 and ABI5 in the regulation ofDOG1 transcript expression is discussed. Other species of the monophyletic genusLepidium showed coat or embryo dormancy and are therefore highly suited for comparative seed biology.

... DOG1是与种子休眠相关的关键基因, 其受ABA调控^[18,20] ...

2013

0.0

. 2013, 67(3):883-893

PLEIOTROPY IN THE WILD: THE DORMANCY GENEDOG1 EXERTS CASCADING CONTROL ON LIFE CYCLES

George C. K. Chiang¹,Deepak Barua^1,2,Emily Dittmar¹,Elena M. Kramer¹,Rafael Rubio de Casas^1,3,Kathleen Donohue^1,4,5

¹ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
² Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
³ National Evolutionary Synthesis Center, Durham, North Carolina 27705
⁴ Department of Biology, Duke University, Durham, North Carolina 27708
⁵ E-mail:k.donohue@duke.edu

In the wild, organismal life cycles occur within seasonal cycles, so shifts in the timing of developmental transitions can alter the seasonal environment experienced subsequently. Effects of genes that control the timing of prior developmental events can therefore be magnified in the wild because they determine seasonal conditions experienced by subsequent life stages, which can influence subsequent phenotypic expression. We examined such environmentally induced pleiotropy of developmental-timing genes in a field experiment withArabidopsis thaliana. When studied in the field under natural seasonal variation, anA. thaliana seed-dormancy gene,Delay Of Germination 1 (DOG1), was found to influence not only germination, but also flowering time, overall life history, and fitness. Flowering time of the previous generation, in turn, imposed maternal effects that altered germination, the effects ofDOG1 alleles, and the direction of natural selection on these alleles. Thus under natural conditions, germination genes act as flowering genes and potentially vice versa. These results illustrate how seasonal environmental variation can alter pleiotropic effects of developmental-timing genes, such that effects of genes that regulate prior life stages ramify to influence subsequent life stages. In this case, one gene acting at the seed stage impacted the entire life cycle.

... 最新研究表明DOG1不仅影响萌发还影响开花时间, 进而影响植物整个生命过程和适应能力^[21] ...

2004

0.0

Chin Sci Bull. 2004, 49(13):1219-1225

The origin and evolution of new genes

Li X , 李昕), Yang S , 杨爽), Peng L-X , 彭立新), Wang W

随着基因组数据的大量积累, 人们愈加认识到各种有机体中基因数目的巨大差异. 这些差异的存在表明, 新基因如何产生不仅是一个重要的进化生物学问题, 也是生命科学中面临的一个基本问题. 对新基因起源机制的探索, 可以追溯到大半个世纪以前, 然而直到上世纪90年代第一个年轻基因——精卫基因(jingwei)的发现, 才使以实证方法研究新基因起源的分子机制成为可能. 此后的10多年中又陆续发现一些新的年轻基因的例子, 对这些基因起源与进化的研究极大地丰富了人们在这一领域的认识. 但目前有限的例子难以从整体的水平对基因组中新基因产生的速率以及新基因的产生对原基因组的影响等问题作出解答. 我们正致力于在基因组的水平寻找更多年轻基因的实例, 以期总结新基因起源与进化的一般规律.

... 外显子捕获、重排和融合是新基因产生的进化机制之一^[22] ...