Nestlé R&D Center, 101 Av. Gustave Eiffel, Notre Dame D'Oé, BP 49716, 37097, Tours, France.
Planta. 2012 Jul;236(1):313-26. doi: 10.1007/s00425-012-1613-2. Epub 2012 Feb 21.
Phenylalanine ammonia lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway producing phenolics, widespread constituents of plant foods and beverages, including chlorogenic acids, polyphenols found at remarkably high levels in the coffee bean and long recognized as powerful antioxidants. To date, whereas PAL is generally encoded by a small gene family, only one gene has been characterized in Coffea canephora (CcPAL1), an economically important species of cultivated coffee. In this study, a molecular- and bioinformatic-based search for CcPAL1 paralogues resulted successfully in identifying two additional genes, CcPAL2 and CcPAL3, presenting similar genomic structures and encoding proteins with close sequences. Genetic mapping helped position each gene in three different coffee linkage groups, CcPAL2 in particular, located in a coffee genome linkage group (F) which is syntenic to a region of Tomato Chromosome 9 containing a PAL gene. These results, combined with a phylogenetic study, strongly suggest that CcPAL2 may be the ancestral gene of C. canephora. A quantitative gene expression analysis was also conducted in coffee tissues, showing that all genes are transcriptionally active, but they present distinct expression levels and patterns. We discovered that CcPAL2 transcripts appeared predominantly in flower, fruit pericarp and vegetative/lignifying tissues like roots and branches, whereas CcPAL1 and CcPAL3 were highly expressed in immature fruit. This is the first comprehensive study dedicated to PAL gene family characterization in coffee, allowing us to advance functional studies which are indispensable to learning to decipher what role this family plays in channeling the metabolism of coffee phenylpropanoids.
苯丙氨酸解氨酶（PAL）是苯丙烷途径的第一个酶，可产生广泛存在于植物性食品和饮料中的酚类化合物，包括绿原酸和多酚。在咖啡豆中，这些多酚含量极高，长期以来被认为是强大的抗氧化剂。迄今为止，虽然 PAL 通常由一个小基因家族编码，但在经济上重要的栽培咖啡品种中，仅对 Coffea canephora （CcPAL1）的一个基因进行了特征描述。在这项研究中，基于分子和生物信息学的搜索成功地鉴定出了两个额外的基因，CcPAL2 和 CcPAL3，它们具有相似的基因组结构，编码的蛋白质序列也很接近。遗传作图有助于将每个基因定位在三个不同的咖啡连锁群中，特别是 CcPAL2，它位于咖啡基因组连锁群（F）中，该连锁群与含有 PAL 基因的番茄染色体 9 区域同源。这些结果与系统发育研究相结合，强烈表明 CcPAL2 可能是 C. canephora 的祖先基因。还对咖啡组织进行了定量基因表达分析，结果表明所有基因都具有转录活性，但它们的表达水平和模式存在差异。我们发现 CcPAL2 转录本主要出现在花、果实果皮和根和枝条等营养/木质化组织中，而 CcPAL1 和 CcPAL3 在未成熟果实中高度表达。这是首次对咖啡 PAL 基因家族进行全面研究，使我们能够进行功能研究，这对于了解该家族在引导咖啡苯丙烷代谢中的作用至关重要。
