AUTHOR=Luesse Darron R. , Wilson Margaret E. , Haswell Elizabeth S. 

TITLE=RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway

JOURNAL=Frontiers in Plant Science

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2015.01148

DOI=10.3389/fpls.2015.01148

ISSN=1664-462X

ABSTRACT=<p>Determining whether individual genes function in the same or in different pathways is an important aspect of genetic analysis. As an alternative to the construction of higher-order mutants, we used contemporary expression profiling methods to perform pathway analysis on several <italic>Arabidopsis thaliana</italic> mutants, including the <italic>mscS-like</italic> (<italic>msl</italic>)2<italic>msl3</italic> double mutant. MSL2 and MSL3 are implicated in plastid ion homeostasis, and <italic>msl2msl3</italic> double mutants exhibit leaves with a lobed periphery, a rumpled surface, and disturbed mesophyll cell organization. Similar developmental phenotypes are also observed in other mutants with defects in a range of other chloroplast or mitochondrial functions, including biogenesis, gene expression, and metabolism. We wished to test the hypothesis that the common leaf morphology phenotypes of these mutants are the result of a characteristic nuclear expression pattern that is generated in response to organelle dysfunction. RNA-Sequencing was performed on aerial tissue of <italic>msl2msl3</italic><italic>geranylgeranyl diphosphate synthase 1</italic> (<italic>ggps1</italic>), and <italic>crumpled leaf</italic> (<italic>crl</italic>) mutants. While large groups of co-expressed genes were identified in pairwise comparisons between genotypes, we were only able to identify a small set of genes that showed similar expression profiles in all three genotypes. Subsequent comparison to the previously published gene expression profiles of two other mutants, <italic>yellow variegated 2</italic> (<italic>var2</italic>) and <italic>scabra3</italic> (<italic>sca3</italic>), failed to reveal a common pattern of gene expression associated with superficially similar leaf morphology defects. Nor did we observe overlap between genes differentially expressed in <italic>msl2msl3, crl</italic>, and <italic>ggps1</italic> and a previously identified retrograde core response module. These data suggest that a common retrograde signaling pathway initiated by organelle dysfunction either does not exist in these mutants or cannot be identified through transcriptomic methods. Instead, the leaf developmental defects observed in these mutants may be achieved through a number of independent pathways.</p>