To decipher the molecular defect in d53, we isolated D53 by a map-based cloning approach. Using an F2 population of ~ 12,000 plants generated from the cross between Ketan Nangka and the mutant, we further delimited the D53 locus to a 34-kb DNA region on the BAC clone OSJNBa0032J07, which contains three putative genes . Sequence analysis revealed a single-nucleotide substitution and 15 nucleotides deletion in the third exon of LOC_Os11g01330 in d53, which resulted in an amino acid substitution and deletion of five amino acids . To verify that this mutation caused the tillering dwarf phenotype, we generated transgenic plants expressing the wild type or mutant D53 gene under the control of rice Actin1 promoter, in a wild-type background. Strikingly, all transgenic plants expressing the mutant d53 gene showed a more exaggerated tillering phenotype than those expressing the wild-type D53 gene. The severity of tillering phenotype in these transgenic plants was correlated with the expression level of the transgene. Notably, overexpression of the wild-type D53 gene also caused a moderate increase in tillering, compared to the vector control plants . These observations suggested that the D53 protein acts as a repressor in the SL-mediated branching-inhibition pathway and that the dominant tillering phenotype of the d53 mutant was most likely caused by a gain-of-function mutation in d53. To further confirm this, we generated D53 knockdown transgenic plants using a RNA interference approach. As expected, reducing D53 expression in d53 background drastically reduced the tiller number . Taken together, these data support the proposition that d53 mutation enhanced D53 activity in repressing SL signaling. D53 is predicted to encode a protein of 1131 amino acids. A BLAST search identified a closely related homolog of D53 with 96.6% amino acid sequence identity in the rice genome. In addition, D53 homologs were found in other monocots and dicots, but not in lower plants, animals or microbes, indicating that D53- like proteins are specific in higher plants . Sequence analysis by the HHpred structure prediction server revealed that D53 shares a similar secondary structure composition, despite low primary sequence homology, to proteins of the class I Clp ATPases family, hydroponic channel which are characterized by an N-terminal domain, a D1 ATPase domain, an M domain, and a D2 ATPase domain36.
Notably, the D2 domain of D53 contains a highly conserved linear sequence, FDLNL, which closely matches the ETHYLENE RESPONSE FACTOR-associated amphiphilic repression motif , which is known to interact with the TOPLESS family of proteins and involved in transcriptional repression37 . Real-time PCR analysis revealed that D53 was widely expressed in the examined rice tissues . D53 promoter driven GUS reporter gene assay showed that GUS staining was observed in vasculature in roots, shoots, leaves, leaf sheaths, nodes, internodes and young panicles, preferentially in the parenchyma cells surrounding the xylem . Moreover, D53 expression was up-regulated by GR24 treatment in wild-type plants, but down-regulated in six d mutants, suggesting that expression of D53 is regulated by SLs signaling . The D53-GFP fusion protein is exclusively localized to the nucleus in rice protoplasts and the pActin::D53-GFP transgenic root cells . Previous studies have identified the F-box protein D3 and the α/β hydrolase D14 as two key components of SL signaling in rice10,12, of which D14 and its orthologues in Arabidopsis and Petunia have been proposed to directly participate in SL perception 19,27,28. Yeast two-hybrid assay showed that both D53 and d53 could physically interact with D14 in the presence of GR24 . Domain deletion analysis indicated that the D1 domain of D53 was essential for the GR24-dependent D53-D14 interaction. Interestingly, its binding activity was inhibited by the M and D2 domains, although their negative effect can be overcome by the N domain . We verified the D53-D14 interaction in N. benthamiana leaf cell nucleus both in the presence or absence of exogenously applied GR24 using a bimolecular fluorescence complementation assay . The observed interaction between D53 and D14 in the absence of exogenously applied GR24 might be due to the effect of endogenous SLs present in the tobacco leaf cells. Consistent with the previously reported GR24-depedent interaction between DAD2 and PhMAX2A in yeast19, our in vitro pull down assay also revealed a direct physical interaction between D14 and D3 in a GR24- dependent manner . Furthermore, using recombinant GST-D3-OSK1 fusion protein as the bait, our in vitro pull-down assay showed that D14 could be more efficiently coimmuno precipitated from d3 plant extracts in the presence of exogenously applied GR24 . Together, these results suggest that SLs may act to promote complex formation among D14, D3 and D53, linking D53 to the hormone-perception components of the SL signaling pathway. To investigate how SL regulates D53, we performed a set of additional experiments. Both western blot analysis and fluorescence microscopy examination showed that GR24 treatment induced rapid degradation of the D53 protein in wild-type cells, but not in d3 and d14 mutant cells . We further showed that D53 was degraded by the proteasome, as a proteasome inhibitor, MG132, but not other protease inhibitors, effectively blocked GR24-induced D53-GFP degradation . Notably, unlike the wild-type D53-GFP fusion protein, the mutant d53-GFP fusion protein appeared to be stable in the presence of GR24 . Interestingly, we noted that D53-GFP and D53-LUC were still degraded in the d53 mutant cells, but not in d3 or d14 mutant cells , indicating that the D53 degradation pathway was still operational in the d53 mutant.
Together, these results suggest that SL triggers proteasome-mediated degradation of D53 in a D14- and D3-dependent manner. Importantly, the insensitivity of d53 protein to SL-triggered turnover is consistent with the observed dominant gain-of-function mutant phenotype of d53. To provide genetic support for the functional relationship between D53, D3 and D14, we generated d3 d53 and d14 d53 double mutants. The d3 mutant had more tillers and it was shorter than the d14 and d53 single mutants . The d14 d53 double mutants exhibited a dwarf tillering phenotype resembling the d14 and d53 parental plants, whereas the d3 d53 double mutant exhibited a dwarf tillering phenotype resembling d3 . The lack of obvious additive effects among these mutants suggests that D3, D14 and D53 act in the same signaling pathway. To further test their epistasis relationship, we knocked down D53 gene expression in the d3 and d14 backgrounds. As shown in Fig. 4g and Extended Data Fig. 9b–d, the mutant phenotype of d3 and d14 was restored to nearly wild type levels, demonstrating that D53 acts downstream of D3 and D14, and that accumulation of D53 protein is responsible for blocking SL signaling and conferring the dwarf tillering phenotype in these mutants. It has been speculated that perception of SLs triggers the degradation of putative repressors by the SCFMAX2 ubiquitin ligase complex to suppress shoot branching21,29,30. In this study, we established that D53 acts as a repressor of SL signaling in rice. Consistent with the previous observation of GR24-dependent interaction between DAD2 and PhMAX2 , we found that GR24 also promotes the interaction between D14 with D53 and D3 . Further, we showed that D53 is targeted for degradation by the proteasome in a D14- and D3-dependent manner . Together, these data collectively support the notion that SL perception by D14 acts to promote ubiquitination of D53 by the D14-SCFD3 ubiquitin ligase, and subsequent degradation of D53 by the proteasome, leading to the propagation of SL signal and downstream physiological responses . Our findings revealed a remarkable similarity between the hormonal perception and signaling mechanism of SL and several other classes of plant hormones, including auxin, jasmonate and gibberellin25,38–40 . Interestingly, a recent study reported that a D53 homologue in Arabidopsis, SMAX1, acts downstream of MAX2 in repressing the seed germination and seedling photomorphogenesis phenotypes of max2, but not the lateral root formation, axillary shoot growth, or senescence phenotypes of max2 . Further, as observed for D53, three closest homologs of D53 in Arabidopsis were also induced by GR24 treatment41, suggesting that D53 and its homologues play a broad role in regulating different developmental processes and that the D3/D53 functional module is conserved between monocots and dicots. Consistent with this notion, the SL-analogous compounds karrikins also employ a MAX2 and KAI2 – dependent pathway to regulate seed germination and seedling growth29,42. The identification and characterization of D53 in SL signaling now set the stage for further dissection of the mechanisms by which SLs regulate plant form and its complex interactions with parasitic weeds and symbiotic arbusular mycorrhizal fungi3 .According to the United Nations, the population of the world is expected to grow in the next century, which in turn encourages the development of innovative techniques to ensure agricultural sustainability. Agriculture on productive land is threatened not only by high levels of urbanization, uneven water distribution, hydroponic dutch buckets and inclement weather, but also is threats to biodiversity that have unfavorable environmental impacts.
Due to the anticipated drastic population growth and constraints on resources in the upcoming decades, only 10% of the demand for food is estimated to be met by expansion of productive lands, with the remainder relying on new techniques that can achieve higher yields. Therefore, developing novel methods to augment the ratio of crop production over used land is a vital issue. In recent years, the indoor vertical farming systems with artificial light are found to be a viable solution to resolve the in-creasing demands of future agricultural products. The IVFS are promising alternatives to open field or greenhouse agriculture because they have precisely monitoring environmental parameters and are insensitive to outdoor climates, which can boost annual sales volume per unit area up to 100 times compared to that of open lands. Furthermore, employment of light emitting diodes as light sources can initiate and sustain photosynthesis reactions and the optical wavelength, light intensity, and radiation intervals can further enhance growth quality. Recently, many studies have been carried out to investigate how environmental parameters, such as closed-loop control, ultrasound, and electro-degradation, affect hydroponic cultivation of leafy vegetables in these systems. One of the most influential factors affecting growth in IVFS is to maintain a uniform air flow at an optimal air current speed over plants canopy surfaces.It has been found that inducing a horizontal air speed of 0.3–0.5 m s−1 boosts photosynthesis through more efficiently exchanging species between the stomatal cavities in plants and the flow of air. Lee et al. studied the effects of air temperature and flow rate on the occurrence of lettuce leaf tip burn in a closed plant factory system. Furthermore, it was observed that the relative humidity of the air flow can significantly influence calcium transportation in lisian thus cultivars. According to Vanhassel et al., higher levels of relative humidity can significantly decrease the occurrence of tip burn. Therefore, it is vital to maintain relative humidity in the desired range to ensure even distribution of calcium in lettuce leaves. Over the past few years, researchers have been trying to develop techniques for improving uniformity over cultivation zones. Regardless of the recent progress, the control and automation systems of IVFS bring additional costs, which makes systematic experimental investigation and optimization a challenge. Computational fluid dynamics has been utilized as a reliable tool to numerically simulate complex physical phenomena. Markatos et al. developed a CFD procedure to study velocity and temperature distribution in enclosures using buoyancy-induced physics. Stavrakakis et al. investigated the capability of three Reynolds Averaged Navier-Stokes models to simulate natural ventilation in buildings. Papakonstantinou et al. presented a mathematical model for turbulent flow and accordingly developed a 3- D numerical code to compute velocity and temperature fields in buildings. A novel gas-liquid mass transfer CFD model was developed by Li et al. to simulate the absorption of CO2 in a micro-porous micro-channel reactor. Yuan et al. visualized the air paths and thermal leakages near a complex geometry using a transient thermal model with buoyancy-driven convection, conduction and thermal radiation heat transfer and flow field near a vehicle structure. In the context of agriculture, researchers have extensively employed CFD analysis for study of ventilation, air flow, and microclimate in indoor systems. Zhang et al. developed a CFD simulation to assess single-phase turbulent air stream in an indoor plant factory system and achieved the highest level of flow uniformity with two perforated tubes.