Functional analysis of the secondary cell wall (SCW) transcriptional network in Eucalyptus:  Transcriptional networks underlie all developmental processes in eukaryotes.  Complex transcriptional networks regulate genes involved in the deposition of secondary cell wall (SCW) material during wood formation in plants (pictured).  These networks are semi-hierarchical, owing to high interconnectedness and feedback via various levels, which leads to developmental regualtion of SCW structural genes including cellulose, xylan and lignin biosynthetic genes.  We are using cutting-edge next-generation sequencing approaches (chromatin immunoprecipitation and next-generation DNA sequencing) and yeast-based methods (yeast 1-hybrid, yeast 2-hybrid) to study key transcription factors controlling biopolymer synthesis in developing wood in Eucalyptus.  An understanding of eucalypt transcriptional networks provides an avenue to improve wood properties through strategic modification (rewiring) of transcriptional networks regulating traits of commercial interest.


Interactions modulating the transcriptional regualtion of wood formation:  This research focuses on elucidating the protein-DNA and protein-protein interactions comprimising the SCW transcriptional regulatory work.   One of the goals is toidentify conserved regulatory sequences involved in modulating the expression of the structural genes using reporter gene in insilico analyses.  In order to identify proteins involved in protein-DNA interactions, we cloned several full-length cDNAs from the Eucalyptus SCW regulatory network to form a panel of transcription factors that can be creened against promoter sequences of cellulose, xylan and lignin biosynthesis genes.  This panel of transcription factors were used to successfully identify proteins that may modulate cellulose synthase gene expression in Eucalyptus.


Functional genetics of SCW-related proteins of unknown function:  Despite considerable effort, the function of hundreds of genes involved in cell wall biosynthesis, functional characterisation of genes implicated in this biologically important process is necessary.  Although the function of many genes and the proteins they code can be predicted by comparative genomics, domain identificaiton and gene expression analysis, there are still classes of proteins whose function cannot be predicted using current technologies and information.  In recent years, the importance of these proteins (referred to as Cell Wall-related Proteins of Unkown Function(s) or CW-PUFs) has become evident.  This research project focuses on the identificaiton (through systems genetics, comparative genomics and functional genomics) and funcitonal characterisation of CW-PUFs to bridge the gap in our molecular understanding of cell wall biology.


Functional analysis of the Eucalyptus pathogen defence genes:  The non-expressor of pathogenesis-related 1(NPR1) gene has previously been demonstrated to confer enhanced tolerance to various pathogens when over-expressed in crop plants.  We have identified four potential NPR1 genes in the Eucalyptus grandis genome based on a bioinformatics approach.  Two of the candidate genes possess the functional domains required for the correct functioning of the gene.  We have set out to over-express the EucalyptusNPR1 gene candidates in the Arabidopsis knock-out mutant (npr1).  In the event that the mutant is complemented, and a resistant phenotype to bacterial and fungal pathogens is restored, we would be confident that the candidate EucalyptusNPR1 gene is a functional regulator of broad spectrum defence and would be an attractive target to manipulate in Eucalyptus.