Background: Calcium-dependent protein kinases (CDPKs) have been shown to play important roles in various physiological processes, including plant growth and development, abiotic and biotic stress responses and plant hormone signaling in plants. Results: In this study, we performed a bioinformatics analysis of the entire maize genome and identified 40 CDPK genes. Phylogenetic analysis indicated that 40 ZmCPKs can be divided into four groups. Most maize CDPK genes exhibited different expression levels in different tissues and developmental stages. Twelve CDPK genes were selected to respond to various stimuli, including salt, drought and cold, as well as ABA and H₂O₂. Expression analyses suggested that maize CDPK genes are important components of maize development and multiple transduction pathways. Conclusion: Here, we present a genome-wide analysis of the CDPK gene family in maize for the first time, and this genomic analysis of maize CDPK genes provides the first step towards a functional study of this gene family in maize.

ETHYLENE-INSENSITIVE 3/ETHYLENE-INSENSITIVE 3-LIKEs (EIN3/EILs) are important ethylene response factors during fruit ripening. Here, we discovered that EIL2 controls carotenoid metabolism and ascorbic acid (AsA) biosynthesis in tomato (Solanum lycopersicum). In contrast to the red fruits presented in the wild type (WT) 45 days after pollination, the fruits of CRISPR/Cas9 eil2 mutants and SlEIL2 RNAi lines (ERIs) showed yellow or orange fruits. Correlation analysis of transcriptome and metabolome data for the ERI and WT ripe fruits revealed that SlEIL2 is involved in β-carotene and AsA accumulation. ETHYLENE RESPONSE FACTORs (ERFs) are the typical components downstream from EIN3 in the ethylene response pathway. Through a comprehensive screening of ERF family members, we determined that SlEIL2 directly regulates the expression of four SlERFs. Two of these, SlERF.H30 and SlERF.G6, encode proteins that participate in the regulation of LYCOPENE-β-CYCLASE 2 (SlLCYB2), encoding an enzyme that mediates the conversion of lycopene to carotene in fruits. In addition, SlEIL2 transcriptionally repressed L-GALACTOSE 1-PHOSPHATE PHOSPHATASE 3 (SlGPP3) and MYO-INOSITOL OXYGENASE 1 (SlMIOX1) expression, which resulted in 1.62 fold increase of AsA via both the L-galactose and myoinositol pathways. Overall, we demonstrated that SlEIL2 functions in controlling β-carotene and AsA levels, providing a potential strategy for genetic engineering to improve the nutritional value and quality of tomato fruit.

The transition of plants to land required several regulatory adaptive mechanisms. Little is known about these mechanisms, but they no doubt involved the evolution of transcription factor (TF) families. ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) transcription factors (TFs) are core components of the ethylene signaling pathway that play important roles in almost every aspect of plant development and environmental responses by regulating the transcription of numerous genes. However, the evolutionary history of EIN3/EIL TFs, which are present in a wide range of streptophytes, is still not clear. Here, to explore the evolution and functions of EIN3/EIL TFs, we performed phylogenetic analysis of these TFs and investigated their gene and protein structures as well as sequence features. Our results suggest that the EIN3/EIL TF family was already was already present in the ancestor of streptophyte algae. Phylogenetic analysis divided the EIN3/EIL TFs into three groups (Group A–C). Analysis of gene and protein structure revealed that most of the structural features of these TFs had already formed in ancient lineages. Further investigation suggested that all groups have undergone several duplication events related to whole-genome duplications in plants, generating multiple, functionally diverse gene copies. Therefore, as plants colonized terrestrial habitats and evolved key traits, the EIN3/EIL TF family expanded broadly via multiple duplication events, which could have promoted their fundamental neo- and sub-functionalization to help plants adapt to terrestrial life. Our findings shed light on the functional evolution of the EIN3/EIL TF family in the streptophytes.

Intramembrane proteases play very important roles in plants, such as chloroplast development, flower morphology, and response to abiotic stress. In this study, a putative metalloprotease gene, homologous to Ethylene-dependent Gravitropism deficient and Yellow-green2 (EGY2) of Arabidopsis, was isolated from tomato (Solanum lycopersicum) plants and named SlEGY2. We found that SlEGY2 was a member of the metalloprotease family M50 which contained conserved motifs HEXXH and NPDG and was localized in the chloroplast. SlEGY2 antisense transgenic tomato plants (AS) have similar hypocotyls phenotype to the Arabidopsis egy2 mutant. Heat (42 °C), PEG, ABA and MeJA treatments can upregulate the expression of SlEGY2. Under heat stress, SlEGY2 AS lines are more sensitive, with more water loss (lower fresh weight), seriously damaged membrane, and ROS accumulation, but lower activities of APX and CAT. In addition, suppression of SlEGY2 decreases the content of chlorophyll and photosynthetic activities, especially photosystem II. These results suggest that SlEGY2 can regulate the thermotolerance of tomatoes by affecting ROS accumulation and photosynthetic activities.

Precursor mRNA (pre-mRNA) splicing occurs co-transcriptionally and is coupled to transcription through the coordinated assembly of the splicing and transcription machinery. Splicing factor 3B subunit 2 (SF3B2) plays a critical role in pre-mRNA splicing and facilitates spliceosome assembly in humans, but its function in plants remains unclear. Here, we demonstrate that the Arabidopsis thaliana SF3B2 homolog AtSF3B2 interacts with the splicing factors AtU2AF65B and AtSYF2 via its conserved DUF382 domain. As a negative regulator of floral transition, AtSF3B2 binds to pre-mRNAs and modulates the splicing of its target genes, including the central floral repressor FLOWERING LOCUS C (FLC), its antisense transcript COOLAIR, and their regulator WRKY63. Furthermore, AtSF3B2 promotes the transcription of these genes by interacting with the RNA polymerase II (Pol II) subunit NRPB12 and by binding directly to DNA to influence Pol II enrichment. RNA sequencing analyses reveal that the AtSF3B2 mutation predominantly results in intron retention and exon skipping, especially for shorter exons with a lower GC content. A subset of flowering regulators, including FLM, was identified as an AtSF3B2 target. Additionally, AtSF3B2 functions in high temperature-dependent flowering by modulating transcription and splicing of FLM. Together, our findings reveal transcriptional and post-transcriptional roles for AtSF3B2 in the flowering transition.