A novel BSD domain-containing transcription factor controls vegetative growth, leaf senescence, and fruit quality in tomato

The SINA1-BSD1 Module Regulates Vegetative Growth Involving Gibberellin Biosynthesis in Tomato

In plants, vegetative growth is controlled by synergistic and/or antagonistic effects of many regulatory factors. Here, the authors demonstrate that the ubiquitin ligase seven in absentia1 (SINA1) mammalian BTF2-like transcription factors, Drosophila synapse-associated proteins, and yeast DOS2-like proteins (BSD1) function as a regulatory module to control vegetative growth in tomato via regulation of the production of plant growth hormone gibberellin (GA). SINA1 negatively regulates the protein level of BSD1 through ubiquitin-proteasome-mediated degradation, and the transgenic tomato over-expressing SINA1 (SINA1-OX) resembles the dwarfism phenotype of the BSD1-knockout (BSD1-KO) tomato plant. BSD1 directly activates expression of the BSD1-regulated gene 1 (BRG1) via binding to a novel core BBS (standing for BSD1 binding site) binding motif in the BRG1 promoter. Knockout of BRG1 (BRG1-KO) in tomato also results in a dwarfism phenotype, suggesting BRG1 plays a positive role in vegetative growth as BSD1 does. Significantly, GA contents are attenuated in transgenic SINA1-OX, BSD1-KO, and BRG1-KO plants exhibiting dwarfism phenotype and exogenous application of bioactive GA3 restores their vegetative growth. Moreover, BRG1 is required for the expression of multiple GA biosynthesis genes and BSD1 activates three GA biosynthesis genes promoting GA production. Thus, this study suggests that the SINA1-BSD1 module controls vegetative growth via direct and indirect regulation of GA biosynthesis in tomato.

The potato RNA metabolism machinery is targeted by the cyst nematode effector RHA1B for successful parasitism

The potato (Solanum tuberosum) cyst nematode Globodera pallida induces a multinucleate feeding site (syncytium) in potato roots as its sole source of nutrition. Here, we demonstrate that the G. pallida effector RING-H2 finger A1b (RHA1B), which is a functional ubiquitin ligase, interferes with the carbon catabolite repression 4 (CCR4)-negative on TATA-less (NOT) deadenylase-based RNA metabolism machinery that regulates syncytium development in G. pallida-infected potato. Specifically, RHA1B targets the CCR4-associated factor 1 (CAF1) and StNOT10 subunits of the CCR4-NOT complex for proteasome-mediated degradation, leading to upregulation of the cyclin gene StCycA2 involved in syncytium formation. The StCAF1 subunit of CCR4-NOT recruits the RNA binding protein StPUM5 to deadenylate StCycA2 mRNA, resulting in shortened poly-A tails of StCycA2 mRNA and subsequently reduced transcript levels. Knockdown of either subunit (StCAF1 or StNOT10) of the CCR4-NOT complex or StPUM5 in transgenic potato plants resulted in enlarged syncytia and enhanced susceptibility to G. pallida infection, which resembles the phenotypes of StCycA2 overexpression transgenic potato plants. Genetic analyses indicate that transgenic potato plants overexpressing RHA1B exhibit similar phenotypes as transgenic potato plants with knockdown of StNOT10, StCAF1, or StPUM5. Thus, our data suggest that G. pallida utilizes the RHA1B effector to manipulate RNA metabolism in host plants, thereby promoting syncytium development for parasitic success.

Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism, and stress responses

Tomato (Solanum lycopersicum) fruit store carbon as starch during early development and mobilize it at the onset of ripening. Starch accumulation has been suggested to buffer fluctuations in carbon supply to the fruit under abiotic stress, and contribute to sugar levels in ripe fruit. However, the role of starch accumulation and metabolism during fruit development is still unclear. Here we show that the tomato mutant adpressa (adp) harbors a mutation in a gene encoding the small subunit of ADP-glucose pyrophosphorylase that abolishes starch synthesis. The disruption of starch biosynthesis causes major transcriptional and metabolic remodeling in adp fruit but only minor effects on fruit size and ripening. Changes in gene expression and metabolite profiles indicate that the lack of carbon flow into starch increases levels of soluble sugars during fruit growth, triggers a readjustment of central carbohydrate and lipid metabolism, and activates growth and stress protection pathways. Accordingly, adp fruits are remarkably resistant to blossom-end rot, a common physiological disorder induced by environmental stress. Our results provide insights into the effects of perturbations of carbohydrate metabolism on tomato fruit development, with potential implications for the enhancement of protective mechanisms against abiotic stress in fleshy fruit.

The extensin protein SAE1 plays a role in leaf senescence and is targeted by the ubiquitin ligase SINA4 in tomato

Extensins are hydroxyproline-rich glycoproteins and generally play a structural role in cell wall integrity. In this study, we determined a novel role of tomato (Solanum lycopersicum) SENESCENCE-ASSOCIATED EXTENSIN1 (SAE1) in leaf senescence. Both gain- and loss-of-function analyses suggest that SAE1 plays a positive role in leaf senescence in tomato. Transgenic plants overexpressing SAE1 (SAE1-OX) exhibited premature leaf senescence and enhanced dark-induced senescence, whereas SAE1 knockout (SAE1-KO) plants displayed delayed development-dependent and dark-induced leaf senescence. Heterologous overexpression of SlSAE1 in Arabidopsis also led to premature leaf senescence and enhanced dark-induced senescence. In addition, the SAE1 protein was found to interact with the tomato ubiquitin ligase SlSINA4, and SlSINA4 promoted SAE1 degradation in a ligase-dependent manner when co-expressed in Nicotiana benthamiana leaves, suggesting that SlSINA4 controls SAE1 protein levels via the ubiquitin-proteasome pathway. Introduction of an SlSINA4-overexpression construct into the SAE1-OX tomato plants consistently completely eliminated accumulation of the SAE1 protein and suppressed the phenotypes conferred by overexpression of SAE1. Taken together, our results suggest that the tomato extensin SAE1 plays a positive role in leaf senescence and is regulated by the ubiquitin ligase SINA4.

Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling

The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3'end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.

OsbHLHq11, the Basic Helix-Loop-Helix Transcription Factor, Involved in Regulation of Chlorophyll Content in Rice

Photosynthesis is an important factor in determining the yield of rice. In particular, the size and efficiency of the photosynthetic system after the heading has a great impact on the yield. Research related to high-efficiency photosynthesis is essential to meet the growing demands of crops for the growing population. Chlorophyll is a key molecule in photosynthesis, a pigment that acts as an antenna to absorb light energy. Improvement of chlorophyll content characteristics has been emphasized in rice breeding for several decades. It is expected that an increase in chlorophyll content may increase photosynthetic efficiency, and understanding the genetic basis involved is important. In this study, we measured leaf color (CIELAB), chlorophyll content (SPAD), and chlorophyll fluorescence, and quantitative trait loci (QTL) mapping was performed using 120 Cheongcheong/Nagdong double haploid (CNDH) line after the heading date. A major QTL related to chlorophyll content was detected in the RM26981-RM287 region of chromosome 11. OsbHLHq11 was finally selected through screening of genes related to chlorophyll content in the RM26981-RM287 region. The relative expression level of the gene of OsbHLHq11 was highly expressed in cultivars with low chlorophyll content, and is expected to have a similar function to BHLH62 of the Gramineae genus. OsbHLHq11 is expected to increase photosynthetic efficiency by being involved in the chlorophyll content, and is expected to be utilized as a new genetic resource for breeding high-yield rice.