Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation

Ustilago maydis is a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions. U. maydis suppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found that U. maydis induced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which the U. maydis effector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2F and DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.


Analysis of the maize transcriptional response during tumor formation in hyperplasic and hypertrophic cells.
In a previous work we showed that U. maydis-induced maize tumors are constituted of hypertrophic mesophyll tumor (HTT) cells coming from the mesophyll cells and small hyperplasic tumor (HPT) cells coming from the bundle sheath cells 4 . In contrast to the solopathogenic strain SG200 3 , the U. maydis effector deletion mutant SG200Δsee1 fails to induce DNA synthesis and cell division in bundle sheath cells 4 . Consequently, tumors caused by SG200Δsee1 are mainly built of HTT; while the bundle-sheath derived small tumor cells are missing 4 . To determine genes differentially expressed (DE) in each particular tumorous cell type we performed six pairwise comparisons of cell-type specific control mock groups against SG200 or SG200Δsee1 infected cells (Table 1; Supplementary Dataset 1). The highest number of DE genes was observed in the SG200 infected cells (Table 1), either HTT or HPT when compared to uninfected/mock cells (Mock Bundle Sheath, MBS; Mock Mesophyll cells, MMS), indicating that U. maydis infection induces a strong transcriptional maize cell reprogramming, which is in agreement with previous reports 15,20 . SG200Δsee1 infection induces a milder effect in the mesophyll cells; we found less DE genes when we compared SG200Δsee1 to the MMS than to the HTT (Table 1). This is in agreement with the mild SG200Δsee1 tumor phenotype observed, where the bundle sheath structure is largely preserved and the hypertrophic cells are mostly absent 4 . Few DE genes were detected when we compared HTT against HPT, suggesting that many of the DE genes are shared between these two datasets and their expression behaviors are likely similar (Table 1).
More genes are up-regulated than down-regulated in response to SG200 infection in both cell types (Fig. 1A). The largest difference is observed in the HTT dataset where 6,852 are upregulated in contrast to 1,504 downregulated genes (Fig. 1A). To determine a significant change in gene expression we applied an arbitrary absolute Log2  www.nature.com/scientificreports www.nature.com/scientificreports/ Fold Change (log2FC) threshold of 1.5. This cutoff drastically reduced the number of DE genes; however it kept the observed tendency of more genes being upregulated than downregulated (Fig. 1A).
A small number of genes is DE in all considered datasets (67 genes); in contrast, many genes are shared between HTT and HPT datasets (2680 genes, Fig. 1B). HPT contains the highest number of uniquely expressed genes (4553), followed by HTT (3946), and seeTC (101, Fig. 1B). qRT-PCR analysis to proof the consistency of the data has been already shown ( Supplementary Fig. S11 in Matei et al. 4 ).
In summary, the results demonstrate that SG200 infection has a strong effect on gene expression in both mesophyll and bundle sheath cells. This is in line with the observation that tumor formation correlates with a strong cell reprogramming 15 and this may involve the gene expression of otherwise silenced genes. Moreover, the See1 effector seems to have a key role in such response since the number of DE genes is drastically reduced in SG200Δsee1 infected mesophyll cells (seeTC) in comparison to SG200 infected cells (HTT, Fig. 1B). This gene expression profile reflects the phenotype, as SG200Δsee1 infections induce small tumors 4,8 (please refer to Fig. 5 at Matei et al. 4 for histological details of See1´s effect on cell division).

Functional categorization of DE genes in the hyperplasic and hypertrophic cells: Gene Ontology enrichment (GO) analysis.
To explore the nature of the data we analyzed all DE genes for Gene Ontology enrichment (GO) with the web-based agriGO software 39 . The Singular Enrichment Analysis (SEA) revealed a strong and shared enrichment for several GO-terms between HPT and HTT datasets (Supplementary Dataset 2 and Supplementary Table 1). A total of 171 different GO terms were assigned to all five datasets. 101 terms are common between HPT and HTT datasets. In contrast, only 23 GO terms are common between HTT and seeTC datasets, which is interesting as the only difference is the deletion of the See1 effector supporting the strong effect of this protein. We further analyzed the data with Parametric Analysis of Gene set Enrichment (PAGE), which takes the expression levels into account. This analysis showed 163, 77 and 15 GO terms for HPT, HTT and seeTC respectively (Supplementary Dataset 2). The majority of the GO terms found in HTT and seeTC datasets are shared with HPT with exception of 13 unique to HTT and 4 unique to seeTC datasets. These include very diverse functions in HTT and kinase and transferase activities for seeTC (Supplementary Dataset 2 and Supplementary  Table 2).
Since a considerable number of genes were DE genes and unique in each dataset (Table 1 and Fig. 1B), we decided to explore if such gene subsets were also enriched for specific GO terms. After SEA analysis we found 55 HPT and 44 HTT GO enriched terms, out of which 31 are shared (Supplementary Dataset 3). This suggests that similar functions are performed by different genes that are expressed specifically in each cell-type. Also interesting is that fewer GO terms are lost in the HTT dataset, when comparing the terms assigned to the full list of DE genes against unique DE genes (77 full vs. 44 unique), than in the HPT dataset (163 full vs. 55 unique), suggesting that a lot of the functional diversity for HTT is contain/shared within the unique DE genes. Further analysis with PAGE showed 40 GO terms enriched for HPT and only 5 for HTT (Supplementary Dataset 3). These last five terms are shared with HPT dataset and include: GO:0010467-gene expression; GO:0034645-cellular macromolecule biosynthetic process; GO:0009059-macromolecule biosynthetic process; GO:0043229-intracellular organelle and GO:0043226-organelle. The remaining datasets showed no enrichment ( Table 1).
Dissecting of differentially regulated biological processes: MapMan-Bin enrichment analysis. For a more detailed and less redundant functional classification of DE genes a MapMan-Bin enrichment analysis was performed. MapMan is a software tool composed of different modules including a set of Scavangers which assign non-redundant functional categories to a set of given genes, proteins or metabolites and an Image Annotator module which allows the visualization of data on diagrams of biological processes or pathways relying on mapping files created by the scavangers 40,41 . The plant gene function ontology MapMan consist of 34 major bins and is organized as a tree, thus enabling the categorization of gene functions at different levels of generality 41 . Here, we used direct (level one) children of the root node to generate the profiles, counting all annotations by their respective level one. Afterwards we tested for overrepresented terms in the intersection (both terms), difference (one but not the other) and union (either) in mesophyll and bundle sheath datasets infected with SG200 using exact Fischer tests 42 . This analysis showed an overrepresentation of five MapMan-Bins ( Fig. 2A). Terms include chromatin assembly and remodeling (histones, H4-type histone -12.1.5), cell-cycle (regulation cyclins, CYCA-type cyclin -13.1.1.1), protein biosynthesis (translation and elongation, eEF1A aminoacyl-tRNA binding factor -17.4.1), cytoskeleton (microtubular network, kinesin microtubule-based motor protein activities, kinesin-5 motor protein -20.1.3.4) and protein modification (phosphorylation, TKL kinase superfamily -18.9.1). Interestingly, when looking for the expression status of genes annotated with any of these five MapMan-Bins we find genes that are both DE and tissue specific (Fig. 2B). This indicates that while the respective gene functions (MapMan-Bins) are shared and characteristic for both tumor tissues, there are tissue specific DE genes implementing these functions. Based on these results, and the clear implication of the deregulation of cell cycle regulating genes in tumor formation, we further examined the DE genes with particular focus on maize cell cycle genes.
For a general overview of the effect of U. maydis infection in maize mesophyll and bundle sheath cells we generate a metabolic overview map with MapMan 40,41 . The strongest effect is observed in the photosynthetic light reactions section for the HPT dataset, where many genes are downregulated ( Fig. 3 and Supplemental Fig. 1). Comparably, genes involved in starch formation were downregulated in the HPT dataset ( Fig. 3 and Supplemental  Fig. 2). This is in agreement with our previous finding that these cells are depleted from chloroplasts 4 . In contrast, starch formation and degradation related genes were slightly but mostly upregulated in the HTT dataset ( Fig. 3 and Supplemental Fig. 2). This provides a picture of the maize leaf response towards U. maydis infection and supports the hypothesis of HPT working as a strong active sink tissue that stimulates the attraction of nutrient flow from source tissues, which in this case might be partially enabled by HTT 4,43 . For the seeTC dataset we observe mostly strong upregulation in very punctual but overall distributed processes (Fig. 3). (2019) 9:10227 | https://doi.org/10.1038/s41598-019-46734-3 www.nature.com/scientificreports www.nature.com/scientificreports/ In maize, cellulose microfibrils are mainly crosslinked with glucuronoarabinoxylans (GAXs) 44 . During cell elongation in growing tissues the mixed-linkage (1 → 3), (1 → 4)-β-d-glucan appears transiently as the major cross-linking glycan 45 . Analysis of gene expression of cell wall precursors in HPT and HTT datasets show an upregulation for genes involved in the transformation from UDP-D-glucose to: sucrose, UDP-L-rhamnose, UDP-D-galacturonic acid and UDP-D-xylose (Supplemental Fig. 3). Interestingly, the conversion of UDP-D-xylose to UDP-L-arabinose is upregulated in the HPT dataset (Supplemental Fig. 3). This is in agreement with our data which indicate that U. maydis infection change the ratio contents of monosaccharides, increasing arabinose content and reducing xylose 4 .
We have previously shown that tumors develop and expand in between two primary leaf veins where lignin deposition increases defining the tumor borders 4 . Lignification is commonly associated with plant defense response. The HTT dataset shows an upregulation of genes involved in the formation of three important lignin precursors, namely p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol 46,47 (Supplemental Fig. 4).
Tissue-specific regulation of cell-cycle associated genes by U. maydis. The See1 effector is required for the activation of maize cell mitotic division in bundle sheath cells 4,8 . Therefore, we asked if the unique subset of maize cell cycle genes DE in the bundle sheath SG200 infected cells could reflect the processes that are likely See1-driven.
Cell cycle comprises a sequence of events including DNA replication, cell division and growth all of them requiring the precise coordination of several protein complexes 48 . A candidate list of core-cell-cycle genes was generated using the MapMan Bin annotations using Mercator4 V1 and edited based on literature search to include/annotate described maize cell-cycle machinery and core regulator genes 25,29,30,[49][50][51][52][53][54][55][56][57][58][59][60][61] (Supplementary  Table 3). To facilitate the analysis the core DNA replication machinery (pre-replication complex and genes involved in s-phase) is analyzed in the next chapter.
In general, genes that constitute the basic cell cycle machinery appear DE in four out of five datasets after setting a threshold of |log2FC| ≥ 1.5 ( Table 2). The HTT dataset present the highest number of DE genes (22), followed by HPT (12), HTT.vs.seeTC (5) and seeTC (1; Table 2). The maize genome encodes over 50 cyclins, the majority of which remain uncharacterized 62,63 . Three cell cycle related cyclins, namely A-, B-and D-types are DE in the HPT and HTT datasets. A-type cyclins, which normally are involved in S-phase progression, are upregulated in both HPT and HTT datasets. GRMZM2G017081, which encodes for an A2-type cyclin, is upregulated in the HPT dataset, and was found as part of a subnetwork that positively correlates with leaf size and timing traits in maize 64 . Two uncharacterized B-type cyclins appear upregulated in the HPT and HTT datasets. B-type cyclins are key actors in the G2/M transition and expressed in a narrow time window from late to mid M phase 62 . Finally, several D-type cyclins are upregulated in the HTT dataset. D-type cyclins are regarded as G1-specific and proposed to be sensors of growth conditions by integrating internal and environmental cues 48,65 . Particularly, ZmCYCD2;1 has a positive role in the endoreduplication cycle in endosperm 33 . www.nature.com/scientificreports www.nature.com/scientificreports/ Maize contains at least four Retinoblastoma-related (RBR) genes that can be functionally grouped as repressors RBR1/2 and promoters RBR3/4 of the E2F-DP factors, which promote the transcription of genes required for cell cycle progression 34,[66][67][68] . We observe an up-regulation of RBR3/4 genes in the HPT and HTT cells. Additionally E2F/DP coding genes are upregulated in HTT cells (Table 2).
APC13 is upregulated in the HTT dataset. In humans and yeast APC13 is required for efficient cyclin degradation by promoting the association of the APC3 and APC6 subunits, until now APC13 has not been characterized in plants 29 . CDC20 is strongly upregulated in seeTC dataset. CDC20 is a crucial co-activator of APC/C to degrade Securin and CYCB, promoting in this way the onset of anaphase and mitotic exit 29 .
Two CDK subunit (CKS) proteins are upregulated in the HPT and HTT datasets. CKS work as scaffold proteins that serve as adaptors for targeting CDKS to mitotic substrates but in contrast to cyclins, are not required for proper phosphorylation activity [69][70][71] .
Two CDK Inhibitors (CKIs), belonging to different groups are DE in the HPT and HTT datasets. GRMZMM2G013463, which encodes for an uncharacterized SIAMESE gene (SIM) is upregulated in HPT, and a Kip-Related protein (KRP) ZmKRP3, which is upregulated in HTT dataset. ZmKRP3 belongs to a class of KRPs exclusively present in monocotyledonous plants and presents motifs required for the interaction with CDKs and D-type cyclins, shows a PEST sequence required for targeted degradation and does not present a nuclear localization signal 53 . www.nature.com/scientificreports www.nature.com/scientificreports/ In Arabidopsis, there is a concentration-dependent role of ICK/KRPs in blocking both the G1/S cell cycle and entry into mitosis but allowing S-phase progression promoting a switch to endoreduplication 72 . Several of the best-characterized SIAMESE (SIM) and SIAMESE RELATED (SMR) proteins are also involved in the regulation of the transition from the mitotic cell cycle to endoreplication 72,73 . This poses the question if the two distinct CKI upregulated in the different tumorous cell types are inducing different outcomes to give place to hyperplasic or hypertrophic phenotypes. At least our data clearly indicate that nuclear size, which can be proportionally related to endoreduplication, of mesophyll cells infected with SG200 or SG200Δsee1 is increased while bundle sheath nuclear sizes remain unchanged (Fig. 5). This supports the concept of hypertrophy in mesophylls cells being linked to endoreduplication.
The pre-replication complex (pre-RC, before S-phase). The pre-RC is a very important part of the cell cycle as it defines the origins to initiate DNA replication, regulates DNA replication and assures that each daughter cell receives identic DNA copies 51 . Pre-RC members are conserved in all eukaryotes and previous studies have shown that plants core DNA replication machinery is more similar to vertebrates than single celled yeasts [25][26][27] . The pre-RC consist of an initiator to establish the site of replication initiation (ORC), a helicase to unwind DNA (MCM complex), and CDC6 and CDT1, which act synergistically to load the MCM complex 25,51 . The formation of a pre-replication complex (pre-RC) is a key control mechanism occurring before cells enter S-phase 51 .   www.nature.com/scientificreports www.nature.com/scientificreports/ Our analysis shows that DE genes from the core DNA replication genes are found in three of the five datasets (Figs 6 and 7 and Supplementary Table 4), the HPT dataset (11 genes), HTT (22 genes), and SeeTC.vs.HTT (3 genes). In the HPT dataset we found exclusively upregulated ORC5, ORC6, CDC6, CDT1 (b), SLD5, POLE1, RFC1 and RPA1; additionally PSF1 and PCNA1, which are downregulated. In HTT we found exclusively upregulated genes including ORC2, MCM3, MCM4, MCM5, MCM7, MCM10, TOPBP1 (MEI1), POLA3, POLA4, POLD1, POLD3, RFC2, RFC3, RFC4, RPA1, RPA2 and RPA3 25,51 . POLA2 lays down a short RNA/DNA primer in the lagging strand synthesis 25 , and is upregulated in both HPT and HTT datasets. Finally, the comparison of SeeTC.vs.HTT showed a shared upregulation of RPA2 with the HTT and a unique and strong downregulation for one RPA1 gene (Fig. 6), both necessary to stabilize single stranded DNA. In summary, the HTT shows an upregulation of almost all the elements necessary for DNA replication, a characteristic behavior of cells going through endoreduplication (Fig. 7).

The Skp1/Cullin1/F-box complex (SCF) and SGT1 interactors.
The effector protein See1 is transferred from biotrophic U. maydis hyphae into the cytoplasm and, in particular to the nucleus of the host cell 8 . A yeast-2hybrid (Y2H) screen identified a maize homologue of SGT1 (suppressor of G2 allele of skp1) as its partner/target in maize 8 . SGT1 was originally identified as a cell cycle regulator necessary for the kinetochore formation in yeast 74 . It regulates the cell cycle together with Skp1 in two ways, by regulating Skp1 function in the Skp1/Cullin1/F-box complex (SCF), an ubiquitin ligase that controls the degradation of cell cycle regulators  Cell type-specific nuclear size measurements in leaf tissue sections stained with propidium iodide (PI) at major tumor development stages. Data shows nuclear size measurements 4 dpi and 6 dpi in mock treated, SG200 infected and SG200Δsee1 infected PI stained leaf tissue sections. Analyzed cell types included Mesophyll and resulting hypertrophic tumor cells, as well as bundle sheath cells and resulting hyperplasic tumor cells. A minimum of 70 nuclei was measured per tissue type. Results represent the mean ± SD from three independent leaf sections per biological replicate. Two independent biological experiments were performed. Asterisks indicate statistical significance of nuclear size compared to mock treated tissue of the same age. P-values were calculated using the unpaired student's t-test; ***p ≤ 0.001. www.nature.com/scientificreports www.nature.com/scientificreports/ to allow G1-to-S transition, and by promoting the assembly of the centromere-binding complex that initiates kinetochore formation 74,75 .
Due to the important role of SCF in cell cycle regulation and the interaction of one of its subunits (SGT1) with See1, we decided to explore the expression of genes encoding for its components, additionally we included the 359 F-box genes reported by Jia et al. 76 . F-box genes are crucial components of the SCF-ubiquitin ligases and confer substrate specificity, therefore, the higher the number of F-box proteins the more increases the number of potential SCF complexes. Our analysis showed DE genes encoding for SCF subunits in four out of five datasets (Fig. 8). We observe upregulation of SGT1 in the HPT (Fig. 8A). This observation might be relevant considering that See1 interacts with SGT1 and such interaction may have an impact on cell cycle as no hyperplasic cells are formed in maize leaves infected with SG200Δsee1 4 . In contrast, a general absence of SCF-complex activation is observed in SG200Δsee1 compared to SG200 infected mesophyll cells (Fig. 8B,C). 8 F-box genes are upregulated in HPT and 11 F-box genes deregulated in the HTT dataset, from which two are strongly downregulated (Table 3). In the seeTC dataset, 3 F-box genes were strongly upregulated (Table 3). One DE F-box gene (ZmFBX154.1), upregulated in the HPT dataset, has been reported to respond to multiple stresses and may participate in the crosstalk between different signal transduction pathways 76 . The specific function of the majority of the F-box genes in plants remains unclear and only ZmFBX92, which is not DE in our datasets, has been functionally characterized 64,76 .  www.nature.com/scientificreports www.nature.com/scientificreports/ In summary, no strong expression changes in the SCF components were observed in the HPT and HTT datasets (Fig. 8), but DE F-box genes were detected (Table 3). Interestingly, only two F-box genes are both common and upregulated between the HPT and HTT datasets suggesting that the majority of the selective interactions of the SCF complex are specific for each tumor-type. As a consequence, the abundance of key regulatory proteins, among them proteins involved in the regulation of cell cycle, is likely specific for each tumor-type. We conclude that among the DE F-box genes strong candidates involved in the regulation of cell cycle can be found.

The Small ubiquitin-like modifier (SUMO) and the SUMOylation machinery. SUMOylation is
a post-translational modification that consists of the covalent attachment of a SUMO to a substrate protein 77 . SUMOylation regulates the activity of several proteins involved in critical cellular processes such as cell division and transcriptional regulation 77,78 . In yeast the SUMO-conjugating enzyme Ubc9 plays a role in the degradation of S and M-phase cyclins, and the ubiquitin-like specific protease ULP1, is essential for the G2 to M phase transition 79,80 . Furthermore, aberrant SUMOylation of key cell signaling proteins, including tumor suppressors and oncogenes result in deregulation of cell cycle and division, which ultimately leads to cancer 81 . In human cells, it was recently shown that SUMOylation of the APC4 subunit of the APC/C E3 ubiquitin-ligase is crucial for accurate progression of cells through mitosis; furthermore, SUMOylation increases APC/C ubiquitylation activity toward a subset of its targets 82,83 . In plants, SUMOylation has been implicated in several physiological responses and plays an important role to control cell cycle progression [84][85][86][87] . Particularly, the SUMO-E3-ligase AtMMS21 dissociates the E2Fa/DPa complex regulating in this way the G1/S cell cycle progression 88 .

Discussion
The full maize transcriptome analysis of SG200 infected mesophyll and bundle sheath cells has provided us a deeper view in the mechanisms evoked in the formation of maize leaf tumor. Expected responses, such as the alteration of genes involved in the regulation and performance of cell cycle, were differentially regulated in particular tumor cell types. Interestingly, some of the mechanisms observed differed between cell types and mostly reflected the cell behavior (i.e hyperplasic or hypertrophic). In comparison to the wealth of information and studies performed in mammals or yeast, plant cell cycle still requires a lot of study and homologues functionality validation. Such studies are complicated since in plants large families encode for cell cycle regulators 25,26 . It has been suggested that the evolution of larger families coding for CDKs and cyclins might help to provide a new layer of substrate recognition to coordinate the cell cycle with developmental cues 27 . More difficulties arise due to inconsistent nomenclatures, which difficult the comparisons and analysis 27 . A reductionist vision or description of the maize cell cycle would be simply not correct due to the lack of information/characterization of many genes. Most of the here reported genes still require a functional confirmation. However, this report gives some pointers to promising genes that could shed some light on cell cycles processes, i.e. endoreduplication. The identification of functional homologues that keep the network topology to control cell cycle will be crucial for the advance and understanding of this process in maize and other plants. Furthermore, previous comparative studies between plants and humans have identified putative cancer genes 89 . Such studies aim to identify conserved proliferation genes based on expression and transcriptional regulation in healthy tissues. Our study now provides data on cell cycle related genes in a tumorous tissue. Therefore we believe it provides promising candidates to understand tumorigenesis.

Regulation of cell cycle and core-DNA replication machineries by U. maydis infection.
In plants the analysis of cell cycle mutants has revealed that the loss of cell proliferation control is not sufficient to induce tumor development 24 . Furthermore, plants tolerate fluctuations in cell proliferation rates without this promoting tumor formation 24 .
Transcriptional activation of replication proteins (i.e. pre-replication complex) can induce endoreduplication 90 . Two E2F coding genes and one DPA gene are upregulated in HTT ( Table 2). The heterodimer E2F-DP promotes the expression of S-phase genes. Additionally, the majority of the components required for DNA replication are upregulated in the HTT dataset (Figs 5 and 6); this is in agreement with the hypertrophic phenotype observed 4 . Additionally, DPA expression levels have been also reported to correlate positively with final leaf size traits 64 . The RBR protein family is crucial and defined as a core cell cycle control by repressing G1/S phase cell cycle progression. RBR is known as a tumor suppressor and is inactivated in many human cancers 24 . Two RBR maize genes have been well characterized 66,67 , ZmRBR1 has a canonical function as repressor of cell cycle progression while ZmRBR3 promotes the expression of the E2F/DP targets, including the MCM family, required for the initiation of DNA synthesis 67 . Our analysis showed a strong upregulation of ZmRBR4 and ZmRBR3 in both tumor cell types but no alterations in ZmRBR1/2 gene expressions ( Table 2 and Fig. 4). ZmRBR4 has not yet been characterized but its strong expression in both tumor cell-types rather speaks for a positive role in cell cycle progression.  www.nature.com/scientificreports www.nature.com/scientificreports/ CKS2 is upregulated in the hypertrophic HTT cells. CKS2 is frequently overexpressed in human cancers and other malignancies and such overexpression overrides the intra-S-phase checkpoint that blocks DNA replication in response to replication stress 91,92 , it is tempting to speculate that similar to human cancers, CKS2 upregulation allows DNA replication in despite the replication stress.
In eukaryotes there exists an overall similar topology controlling the entry into S-phase, while the control of mitosis through CDK phosphorylation-dephosphorylation cycles appears more diversified 27 . This reflects what we observe in our datasets where HTT "behaviour" fits with the predicted models while the hyperplasic cells or HPT, more dependent in rapid mitotic phases, is somehow more difficult to describe or predict based on the current observations, and therefore the pattern is more difficult to be described.
Endoreduplication can be achieved by elimination of mitosis promoting components in the presence of persistent DNA replication 90 . Several plant biotrophs induce localized host endoreduplication by activating common mechanisms that include the anaphase-promoting complex ad modulation of core cell cycle transcriptional machinery 93 . Despite being a common mechanism in biotroph-plant interactions, little is known about the host proteins and mechanisms manipulated by the biotroph as well as the effectors involved 93 . The hypertrophic (HTT) cells present an upregulation of several D-type cyclins, E2F-DP, ZmRBR3/4 and the full pre-replication machinery, all necessary to support a persistent DNA replication. In this paper we shade some light on potential host protein candidates and the role of the U. maydis effector See1 in the stimulation of the endoreduplication process.
SGT1 is a protein that takes part in two important complexes, HSP90-RAR1-SGT1 and the SCF-E3 ubiquitin-ligase. HSP90-RAR1-SGT1 is essential in NLR-mediated immune responses and mostly localized in the cytoplasm 94 . On the other hand, SCF-E3 ubiquitin-ligase is crucial for the degradation of proteins involved in the regulation of cell cycle, and therefore mostly acting in the nucleus 75 . The upregulation of SGT1 in the HPT cells and the induction of hyperplasia in BS cells, a phenotype clearly absent in the maize leaves infected with SG200Δsee1, suggest that somehow the cell is reading out an absence of the SGT1 component, which could be due to "sequestration" via See1. It is tempting to speculate that See1 somehow fosters the localization of SGT1 into the nucleus, thus promoting the formation of the SCF-complex. Another possibility is that by occluding the phosphorylation site in SGT1 8 , See1 somehow fosters SGT1 interaction with SCF components instead of the HSP90-RAR1-SGT1 complex. This in addition would have on top the advantage of avoiding programmed cell death.

SUMOylation machinery is induced in hyperplasic cells.
In animal models, hyperplasia can result from the reactivation of pathways involved in embryonic development and suppression of terminal differentiation 95 . In humans, gathering evidence shows a close relationship between SUMOylation and cancer development, including progression and metastasis, with direct evidence that the deregulation of the SUMO-pathway affects the proper function of several oncogenes and tumor suppressor genes 96 . Furthermore, the SUMO machinery has been proposed as a cancer biomarker to determine malignant tissues and cancer progression 97 . Our transcriptome analysis suggests that, like in animals, the SUMO machinery members are specifically deregulated in oncogenic tissues.
ZmSCE1f is a representative isotype II of the SCE E2, this isotype is exclusively found in cereals 98 . Remarkably, all isotype II E2s were abundant in dividing tissues hinting a role during cell division 98 . We observe an upregulation of ZmSCE1f in both tumorous cell types, hypertrophic mesophyll cells (HTT) and hyperplasic bundle sheath cells (HPT); remarkably, such upregulation is stronger in the highly dividing hyperplasic cells, further supporting its role in cell division.
In maize, five SUMOs have been identified, three canonical SUMO genes including an identical duplication of SUMO1 (SUMO1a and SUMO1b) and SUMO2, an evolutionarily conserved SUMO variant (SUMO-v), and the cereal-specific DiSUMO-LIKE (DSUL) [98][99][100] . SUMO-v proteins are most closely related to the fungal/animal Rad60-Esc2-Nip45 (RENi) family, which is involved in DNA damage repair 101 . In maize, SUMO-v is expressed at moderate levels in all tissues, but little is known about its function 98 . Due to the conservation of interaction surfaces as the SUMO-Interacting Motif (SIM, which allows noncovalent interaction with SUMO) and β-grasp fold it has been suggested that SUMO-v may work as a recruiting partner or scaffold protein providing a surface for protein-protein interactions 98 .
SIZ1c encodes for a SAP and MIZ/SP-RING type ligase and presents substantial sequence alterations affecting the PHD domain and C-terminal region, with minimal changes to the SAP and MIZ/SP-RING domains 98 . Since PHD domain is important for target recognition and ZmSIZ1c is highly expressed in the endosperm it is likely that such target substrates are endosperm specific 98 . ZmSiz1c is exclusively upregulated in HTT cells; whether similar target substrates normally expressed in the endosperm are awakening in the leaf tumor cells remain to be explored.