An Integrative Approach to Study the Nuclear-Cytoplasmic Interactions (NCI) in Plants

Coordination of nuclear, mitochondrial and chloroplast genes expression is an indispensible three-way interaction in every plant cell. Identifying the components of this complex interaction provides fundamental information that could enable improvement of organismal performance via cytoplasmic engineering techniques. To elucidate the mechanism(s) of action for anterograde (nucleus to organelle) and retrograde (organelle to nucleus) signaling an integrative approach including QTL analysis, epigenomics and transcriptomic techniques in wheat (Triticum aesstivum) and bean (Phaseolus vulgaris) was employed.  Results indicate that methylation pattern of several stress-responsive genes including Mla, A1du and LRR gene family member(s) are under control of cytoplasmic genomes. Furthermore some nuclear-encoded organelle proteins such as malate dehydrogenase and cytochrome P450 are co-regulated by the cytoplasmic-originated signals via an epigenetic regulatory mechanism. Expression comparison among different tissues in bean revealed that most of the mitochondrial encoded electron transfer chain subunits are significantly over-expressed in floral tissues. This over-expression seems to be correlated with the loss of poly-A tail of mitochondrial transcripts leading to their stability. This integrative study sheds new lights on the inter-genomic communications within the same organism; however, the details of this interaction are yet to be identified.