Genetic modification can be an effective strategy for improving the agronomic traits of tomato (Solanum lycopersicum) to meet demands for yield, quality, functional components, and stress tolerance. However, limited numbers of available tissue-specific promoters represent a bottleneck for the design and production of transgenic plants. In the current study, a total of 25 unigenes were collected from an RNA-sequence dataset based on their annotation as being exclusively expressed in five type of tissues of tomato pericarp (outer and inner epidermis, collenchyma, parenchyma, and vascular tissues), and every five unigenes, was respectively selected from each tissue based on transcription expression. The 3-kb 5′ upstream region of each unigene was identified from the tomato genome sequence (SL2.50) using annotated unigene sequences, and the promoter sequences were further analyzed. The results showed an enrichment in T/A (T/A > 70%) in the promoter regions. A total of 15 putative tissue-/organ-specific promoters were identified and analyzed by real-time (RT) quantitative (q) PCR analysis, of which six demonstrated stronger activity than widely used tissue-specific tomato promoters. These results demonstrate how high spatiotemporal and high throughput gene expression data can provide a powerful means of identifying spatially targeted promoters in plants.

Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, the tomato fruit color formation is an intricate biological process that remain elusive. In this work, we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme which may functions in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated to YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allele (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were up-regulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35dpa and 47dpa compared to the red-fruit tomato cultivar (M82). The in vitro and in vivo biochemical analyses indicated YFT3(S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that S126R mutation can impair YFT3 activity. The molecular docking analysis showed that YFT3 allele has higher ability to recruit IPP, but abolishes attachment of the Mg²⁺ cofactor with IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in the yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.

Chitinase is a kind of glycoside hydrolase which is widely distributed in nature and encoded by multiple genes to catalyze the decomposition of chitin, which plays an important role in the molting and pathogen defense of crustaceans. However, the research on chitinase in crustaceans is mainly focused on a few species with economic value. In this study, full-length cDNA sequences of the HtCHT1, HtCHT3 and HtCHT4 genes were cloned from the mudflat crab Helice tientsinensis by RACE, and the sequences were analyzed. The results showed that the full-length 2,229 bp of HtCHT1 gene encoded 627 amino acids, while the full-length 2,191 bp of HtCHT3 gene produced 489 amino acids, and the full-length 3,312 bp of HtCHT4 gene encoded 664 amino acids. Bioinformatics analysis showed that all the obtained chitinase proteins had the glycosyl hydrolase family 18 (GH18) catalytic domain and chitin-binding domain (ChtBD2), furthermore, HtCHT1 and HtCHT4 proteins had signal peptide domains at N-terminal. Phylogenetic analysis showed that different types of chitinase were clustered, and HtCHTs were closely related to chitinases in the Eriocheir sinensis. Expression profile analysis showed that the HtCHT1, HtCHT3 and HtCHT4 were significantly expressed in hepatopancreas. Furthermore, the expression of three genes was significantly up-regulated in hepatopancreas after the Vibrio parahaemolyticus challenge. These results suggested that HtCHT1, HtCHT3 and HtCHT4 were belonged to the CHITINASE gene family in H. tientsinensis and were potentially involved in the antibacterial immune response. This study provides essential information for further research of chitinase in H. tientsinensis and even crustaceans.

The Chinese mitten crab (Eriocheir sinensis) is an important commercial species in China. E. sinensis is typically farmed in rice-crab symbiosis, as an important ecological farming model. However, E. sinensis is often exposed to a high ammonia environment due to the application of nitrogen fertilizers essential for rice growth. We investigated the molecular mechanisms in the gills of E. sinensis exposed to high ammonia at transcriptional and histological levels. We randomly assigned E. sinensis to two groups (control group, CG; ammonia stress group, AG), and gill samples were excised from the CG and AG groups for histopathological and transcriptome analyses. The histopathological evaluation revealed that ammonia stress damaged the gills of E. sinensis. The transcriptome analysis showed that some essential genes, including Xanthine dehydrogenase (XDH), Ubiquitin C-terminal hydrolase-L3 (UCHL3), O-linked N-acetylglucosamine transferase (OGT), Cathepsin B (CTSB), and Ubiquitin-conjugating enzyme E2 W (UBE2W) changed significantly during ammonia exposure. These genes are related to ammonia detoxification, the immune response, and apoptosis. This study demonstrated the molecular response mechanism of E. sinensis gills to ammonia stress at the transcriptional and histological levels. This study provides insight for further study on the molecular mechanism of ammonia stress in crustaceans and supplies technical support for rice crab symbiosis.

Chitin is polymerized from N-Acetyl-d-Glucosamine (GlcNAc) via β-(1,4) glucoside bonds, and the second largest class of polymers in nature after cellulose. Chitinase, a glycoside hydrolase, catalyses the hydrolysis of chitin into GlcNAc, and chitinase is prevalent in chitin-containing organisms, as well as in organisms lacking chitin. It plays crucial roles in various biological processes including chitin degradation, cell wall metabolism and remodelling, maintenance of cell wall integrity and stability, sterilization, insecticidal effects, and digestion. In crustaceans, chitinase participates not only in the moulting process but also in the digestion of chitin-containing food and defence against pathogens. This paper briefly reviews the structure, classification, distribution, and functions of chitinase in crustaceans, aiming to provide insights for future research.