Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta.
Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta.
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DOI：
10.1186/1471-2229-14-47
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发表时间：
2014-02-14
影响因子：
5.3
通讯作者：
Stanbra L
中科院分区：
文献类型：
--
作者：
Strabala TJ;Phillips L;West M;Stanbra L
人们迅速认识到植物肽信号分子数量众多且多种多样，并且已知它们在被子植物的生长和发育中发挥着重要作用。两个密切相关的肽信号分子家族是 CLAVATA3-胚胎周围区域 (CLE) 和 CLE-LIKE (CLEL) 基因，它们编码在分生组织维持和根向重性中发挥作用的分泌肽配体的前体。裸子植物肽信号分子研究进展落后于被子植物。因此，我们试图鉴定裸子植物中的 CLE 和 CLEL 基因，并对这些基因家族与被子植物进行比较分析。我们对 GenBank/EMBL/DDBJ 裸子植物 EST 数据库以及云杉和青云杉基因组进行了荟萃分析，并在柳杉属、松属和云杉属的八个松类植物中鉴定了 93 个假定的 CLE 基因和 11 个 CLEL 基因。预测的针叶树 CLE 和 CLEL 蛋白序列与其在拟南芥中的同源物具有密切的系统发育关系。值得注意的是，在拟南芥 CLE41/44-气管元件分化 (TDIF) 蛋白（一种气管元件（木质部）分化的抑制剂）的假定直向同源物中，活性 CLE 十二肽的完美保存在所有八种针叶树物种中均可见。我们克隆了辐射松 CLE41/44-TDIF 直系同源物。正如预期的那样，这些基因优先在植物的韧皮部中表达，但出乎意料的是，也在分化的气管元件（TE）培养物中表达。令人惊讶的是，这些 TE 分化抑制剂的转录本丰度在 TE 分化早期急剧增加，表明在这些培养物中除了 TE 之外，一些细胞还分化为韧皮部细胞。应用 CLE13 和 CLE41/44 肽抑制辐射松幼苗的根伸长。我们证明两个 CLEL 基因通过编码单独 CLEL 肽的 3' 末端受体外显子交替剪接。 CLE 和 CLEL 基因存在于针叶树中，它们在这些物种中表现出的序列多样性至少与在其他植物物种中一样多。在超过 3 亿年的进化历史中，只有一种 CLE 肽序列在裸子植物和被子植物之间保持 100% 保守，即 CLE41/44-TDIF 肽及其可能的针叶树直系同源物。这些维管发育调节基因在针叶树韧皮部中的优先表达，就像在双子叶植物中一样，表明裸子植物和双子叶植物的次生生长和木材形成的调节非常相似。基于我们的生物信息学分析，我们预测了几种针叶树 CLEL 肽表达调节的新机制，通过选择性剪接导致选择编码单独 CLEL 肽的替代 C 端外显子。
There is a rapidly growing awareness that plant peptide signalling molecules are numerous and varied and they are known to play fundamental roles in angiosperm plant growth and development. Two closely related peptide signalling molecule families are the CLAVATA3-EMBRYO-SURROUNDING REGION (CLE) and CLE-LIKE (CLEL) genes, which encode precursors of secreted peptide ligands that have roles in meristem maintenance and root gravitropism. Progress in peptide signalling molecule research in gymnosperms has lagged behind that of angiosperms. We therefore sought to identify CLE and CLEL genes in gymnosperms and conduct a comparative analysis of these gene families with angiosperms. We undertook a meta-analysis of the GenBank/EMBL/DDBJ gymnosperm EST database and the Picea abies and P. glauca genomes and identified 93 putative CLE genes and 11 CLEL genes among eight Pinophyta species, in the genera Cryptomeria, Pinus and Picea. The predicted conifer CLE and CLEL protein sequences had close phylogenetic relationships with their homologues in Arabidopsis. Notably, perfect conservation of the active CLE dodecapeptide in presumed orthologues of the Arabidopsis CLE41/44-TRACHEARY ELEMENT DIFFERENTIATION (TDIF) protein, an inhibitor of tracheary element (xylem) differentiation, was seen in all eight conifer species. We cloned the Pinus radiata CLE41/44-TDIF orthologues. These genes were preferentially expressed in phloem in planta as expected, but unexpectedly, also in differentiating tracheary element (TE) cultures. Surprisingly, transcript abundances of these TE differentiation-inhibitors sharply increased during early TE differentiation, suggesting that some cells differentiate into phloem cells in addition to TEs in these cultures. Applied CLE13 and CLE41/44 peptides inhibited root elongation in Pinus radiata seedlings. We show evidence that two CLEL genes are alternatively spliced via 3′-terminal acceptor exons encoding separate CLEL peptides. The CLE and CLEL genes are found in conifers and they exhibit at least as much sequence diversity in these species as they do in other plant species. Only one CLE peptide sequence has been 100% conserved between gymnosperms and angiosperms over 300 million years of evolutionary history, the CLE41/44-TDIF peptide and its likely conifer orthologues. The preferential expression of these vascular development-regulating genes in phloem in conifers, as they are in dicot species, suggests close parallels in the regulation of secondary growth and wood formation in gymnosperm and dicot plants. Based on our bioinformatic analysis, we predict a novel mechanism of regulation of the expression of several conifer CLEL peptides, via alternative splicing resulting in the selection of alternative C-terminal exons encoding separate CLEL peptides.
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影响因子：
56.9
作者：
Fletcher, LC;Brand, U;Meyerowitz, EM
通讯作者：
Meyerowitz, EM
影响因子：
4.9
作者：
Lim, Chae Woo;Lee, Young Woo;Hwang, Cheol Ho
通讯作者：
Hwang, Cheol Ho
影响因子：
56.9
作者：
Kondo, Tatsuhiko;Sawa, Shinichiro;Sakagami, Youji
通讯作者：
Sakagami, Youji
影响因子：
11.6
作者：
Fiume, Elisa;Fletcher, Jennifer C.
通讯作者：
Fletcher, Jennifer C.
DOI：
10.1093/bioinformatics/btt178
发表时间：
2013-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Birol I;Raymond A;Jackman SD;Pleasance S;Coope R;Taylor GA;Yuen MM;Keeling CI;Brand D;Vandervalk BP;Kirk H;Pandoh P;Moore RA;Zhao Y;Mungall AJ;Jaquish B;Yanchuk A;Ritland C;Boyle B;Bousquet J;Ritland K;Mackay J;Bohlmann J;Jones SJ
通讯作者：
Jones SJ