A Genomic Approach to Suberin Biosynthesis and Cork Differentiation

Abstract

Cork (phellem) is a multilayered dead tissue protecting plant mature stems and roots and plant healing tissues from water loss and injuries. Cork cells are made impervious by the deposition of suberin onto cell walls. Although suberin deposition and cork formation are essential for survival of land plants, molecular studies have rarely been conducted on this tissue. Here, we address this question by combining suppression subtractive hybridization together with cDNA microarrays, using as a model the external bark of the cork tree (Quercus suber), from which bottle cork is obtained. A suppression subtractive hybridization library from cork tree bark was prepared containing 236 independent sequences; 69% showed significant homology to database sequences and they corresponded to 135 unique genes. Out of these genes, 43.5% were classified as the main pathways needed for cork biosynthesis. Furthermore, 19% could be related to regulatory functions. To identify genes more specifically required for suberin biosynthesis, cork expressed sequence tags were printed on a microarray and subsequently used to compare cork (phellem) to a non-suberin-producing tissue such as wood (xylem). Based on the results, a list of candidate genes relevant for cork was obtained. This list includes genes for the synthesis, transport, and polymerization of suberin monomers such as components of the fatty acid elongase complexes, ATP-binding cassette transporters, and acyltransferases, among others. Moreover, a number of regulatory genes induced in cork have been identified, including MYB, No-Apical-Meristem, and WRKY transcription factors with putative functions in meristem identity and cork differentiation.

A comparative transcriptomic approach to understanding the formation of cork

“…The term 'oxylipins' is also strongly enriched in cork and their role could be related to jasmonic acid accumulation and programmed cell death or senescence (Reinbothe et al 2009). Another explanation for the enrichment of the term 'oxylipins' could be that, as previously suggested by Soler et al (2007), there is a higher epoxidation of suberin monomers catalyzed by lipoxygenases, a family of enzymes that is traditionally related to the biosynthesis of oxylipins.…”

“…For comparative analysis between cork oak phellem and xylem tissues, we used samples collected by Soler et al (2007). For the analysis of cork oak phellem tissue over the growing season we used samples collected by Soler et al (2008).…”

“…The activity of the meristematic phellogen cells is asymmetrical with many more cell layers being produced outwardly than inwardly, resulting in a thicker phellem. Moreover, whereas phelloderm cells are parenchymatous, phellem cells have to undergo several sequential differentiation stages (cell expansion, massive deposition of suberin into their cell walls, and programmed cell death) to reach maturity (Soler et al 2007). In these phellem cells walls, the deposition of suberin, a highly hydrophobic polyester comprised of aliphatic monomers esterified to aromatic compounds (Bernards 2002;Graça and Santos 2007;Pollard et al 2008), provides the periderm with its protective role.…”

“…Over the past decade, a few transcriptomic and proteomic studies have sought relevant genes for periderm formation in cork oak (Soler et al 2007;Ricardo et al 2011). However, deep sequencing technologies such as RNA-seq have recently emerged as powerful tools for obtaining more profound insights into the functional genomics from both model and non-model species, allowing the analysis of the extent and complexity of transcriptomes, the inference of metabolic and regulatory networks, and the identification of candidate genes differentially regulated in a particular condition or developmental stage (Mardis 2008;Wang et al 2010).…”

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…The first genomic approach to suberin biosynthesis and cork differentiation used a suppression subtractive hybridization (SSH) strategy (Soler et al 2007). In that work, a list of candidate genes isolated from cork tissues were identified including genes for the synthesis, transport, and polymerization of suberin monomers as well as a number of regulatory genes including members of the NO APICAL MERISTEM (NAM), MYB and WRKY transcription factor families with putative functions in meristem identity and cork differentiation.…”