Scion, 49 Sala St, PO Box 3020, Rotorua 3010, New Zealand.
BMC Plant Biol. 2014 Feb 14;14:47. doi: 10.1186/1471-2229-14-47.
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.
人们越来越意识到植物肽信号分子数量众多且多种多样，它们在被子植物的生长和发育中起着重要作用。两个密切相关的肽信号分子家族是 CLAVATA3-EMBRYO-SURROUNDING REGION（CLE）和 CLE-LIKE（CLEL）基因，它们编码分泌肽配体的前体，这些配体在分生组织维持和根向重力性中起作用。裸子植物中肽信号分子研究的进展落后于被子植物。因此，我们试图在裸子植物中鉴定 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 数据库和 Picea abies 和 P. glauca 基因组进行了荟萃分析，在 8 种松柏目中的 8 个物种中鉴定出 93 个推定的 CLE 基因和 11 个 CLEL 基因，包括 Cryptomeria、Pinus 和 Picea 属。预测的针叶树 CLE 和 CLEL 蛋白序列与拟南芥同源物具有密切的系统发育关系。值得注意的是，在所有 8 种针叶树中，拟南芥 CLE41/44-TRACHEARY ELEMENT DIFFERENTIATION（TDIF）蛋白的假定同源物的活性 CLE 十二肽都得到了完美的保守，CLE41/44-TDIF 蛋白是木质部（木质部）分化的抑制剂。我们克隆了 Pinus radiata CLE41/44-TDIF 同源物。这些基因在植物体内的韧皮部中优先表达，这是预期的，但出乎意料的是，在分化的木质部（TE）培养物中也表达。令人惊讶的是，这些 TE 分化抑制剂的转录丰度在 TE 分化的早期急剧增加，这表明在这些培养物中，一些细胞除了分化成木质部细胞外，还分化成韧皮部细胞。应用 CLE13 和 CLE41/44 肽抑制 Pinus radiata 幼苗的根伸长。我们提供的证据表明，两个 CLEL 基因通过编码单独的 CLEL 肽的 3'末端受体外显子进行选择性剪接。
CLE 和 CLEL 基因存在于裸子植物中，它们在这些物种中的序列多样性至少与其他植物物种一样多。在 3 亿多年的进化历史中，只有一个 CLE 肽序列在裸子植物和被子植物之间保持了 100%的一致性，即 CLE41/44-TDIF 肽及其可能的针叶树同源物。这些血管发育调节基因在裸子植物韧皮部中的优先表达，就像在双子叶植物中一样，表明在裸子植物和双子叶植物中次生生长和木质部形成的调节具有密切的相似性。基于我们的生物信息学分析，我们预测了几个针叶树 CLEL 肽表达的一种新的调节机制，通过选择性剪接选择编码单独 CLEL 肽的替代 C 末端外显子。
