Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals

Abstract

Endoreduplication is a specialized cell cycle in which DNA replication occurs, but mitosis is skipped creating enlarged polyploid cells. Endoreduplication is associated with the differentiation of many specialized cell types. In the Arabidopsis thaliana sepal epidermis endoreduplicated giant cells form interspersed between smaller cells. Both the transcription factor Arabidopsis thaliana MERISTEM LAYER1 (ATML1) and the plant-specific cyclin dependent kinase inhibitor LOSS OF GIANT CELLS FROM ORGANS (LGO)/SIAMESE RELATED1 (SMR1) are required for the formation of giant cells. Overexpression of LGO is sufficient to produce sepals covered in highly endoreduplicated giant cells. Here we ask whether overexpression of LGO changes the transcriptome of these mature sepals. We show that overexpression of LGO in the epidermis (LGOoe) drives giant cell formation even in atml1 mutant sepals. Using RNA-seq we show that LGOoe has significant effects on the mature sepal transcriptome that are primarily ATML1-independent changes of gene activity. Genes activated by LGOoe, directly or indirectly, predominantly encode proteins involved in defense responses, including responses to wounding, insects (a predator of Arabidopsis), and fungus. They also encode components of the glucosinolate biosynthesis pathway, a key biochemical pathway in defense against herbivores. LGOoe-activated genes include previously known marker genes of systemic acquired resistance such as PR1 through PR5. The defensive functions promoted by LGOoe in sepals overlap with functions recently shown to be transcriptionally activated by hyperimmune cpr5 mutants in a LGO-dependent manner. Our findings show that the cell cycle regulator LGO can directly or indirectly drive specific states of gene expression; in particular, they are consistent with recent findings showing LGO to be necessary for transcriptional activation of many defense genes in Arabidopsis.

Ploidy and Size at Multiple Scales in the Arabidopsis Sepal

“…Live imaging of Arabidopsis sepal pavement cells has shown that endoreduplicating cells grow at the same relative rate, on average, as their dividing neighbors (Tauriello et al, 2015); in essence, endoreduplicated cells are larger because they grow without being halved by division (Roeder et al, 2010). Endopolyploidy has also been linked to cell fate: nascent trichomes in which endoreduplication is blocked often lose their identity (Bramsiepe et al, 2010), and pavement cells differ in gene expression based on their level of endopolyploidy (Roeder et al, 2012;Schwarz and Roeder, 2016). Global transcription increases with endopolyploidy in tomato fruit (Solanum lycopersicum; Bourdon et al, 2012;Pirrello et al, 2018).…”

“…Wild-type Arabidopsis sepals have a pattern of interspersed small, medium, and large (giant) cells with corresponding ploidy 2C-32C ( Figures 2A and 2B, WT) (Roeder et al, 2010). The SIM-related cyclin-dependent kinase inhibitor LGO has been shown to affect the proportion of cells entering endocycles: Overexpression of LGO increases endoreduplication, and loss of function reduces it (Roeder et al, 2010;Schwarz and Roeder, 2016). We have previously shown that the transcription factor MERISTEM LAYER1 (ATML1) affects the proportion of endoreduplicated cells in a dosage-dependent manner;…”

“…We next compared expression responses to WGM with expression responses to endopolyploidy as estimated by RNA-seq data from a LGO dosage series (Schwarz and Roeder, 2016);…”

Functional Analysis of Short Linear Motifs in the Plant Cyclin-Dependent Kinase Inhibitor SIAMESE

“…SMR1/LGO regulates endoreplication in giant cells of the sepal epidermis as well as during leaf development (Roeder et al, 2010), and SMR2 plays a role in the timing of the switch from cell division to endoreplication early in leaf development (Kumar et al, 2015), emphasizing the role of SMRs in controlling endoreplication. SMRs also have been implicated in blocking cell division in response to DNA damage or drought stress and in responses to pathogens (Wang et al, 2014;Yi et al, 2014;Hamdoun et al, 2016;Schwarz and Roeder, 2016;Dubois et al, 2018). Multiple SMRs from Arabidopsis, as well as other plants, can complement the sim trichome phenotype, in which cells divide several times instead of endoreplicating their DNA, indicating that there is an underlying functional similarity among all members of the family tested (Peres et al, 2007;Kumar et al, 2015).…”

Why do plants need so many cyclin-dependent kinase inhibitors?

“…Consistent with such a role of CKIs in plant immune responses, overexpression of SMR1/LGO in the sepal epidermis results in overexpression of a suite of defense-response genes that overlap substantially with the set of genes upregulated in cpr5 mutants. 33 CPR5 appears to be an integral component of the plant nuclear pore complex, and a model for the role of KRPs and SMRs in effector triggered immunity has been proposed in which the CKIs are associated with CPR5 in the nuclear pore complex until released for effector-triggered immune signaling by a conformational change in CPR5 34 It remains to be resolved are how the role of KRPs and SMRs in the mitotic and endoreplication cell cycles, which presumably require free CKIs in the nucleoplasm, are related to this model.…”