Abstract Background Dendrobium officinale Kimura et Migo, a traditional Chinese orchid herb famous for its great horticultural and medicinal value, grows in an adverse habitat and suffers from abiotic or biotic stresses. Sugar metabolism is a vital metabolic process in plants that involves acid invertase. Moreover, the participation of acid invertases in plant responses to environmental stress has also been unveiled. However, the function and structure of the vacuolar invertase gene in Dendrobium officinale remain unclear. Methods and Results In this study, the vacuolar invertase gene ( DoVIN2 ) was cloned from the “DanXia” cultivar of D. officinale using homologous cloning. The cDNA sequence of DoVIN2 was 1368 bp and included a 455-amino-acid protein with a sugar hydrolase domain. The DoVIN2 protein did not possess a signal peptide or transmembrane region, was a hydrophilic stable protein, and contained 46 phosphorylation sites, with high conservation in evolution. The transient green fluorescent protein gene ( GFP ) expression results in rice mesophyll protoplasts demonstrated that DoVIN2 was localized in the cell nucleus. The expression level of the DoVIN2 gene differed significantly among different tissues, with the highest expression in flowers followed by stems, roots, and leaves. Several abiotic stress–responsive elements were present in the promoter region of the DoVIN2 gene. Cold stress and abscisic acid (ABA) treatment upregulated DoVIN2 gene expression, while the expression of DoVIN2 was negatively correlated with polyethylene glycol (PEG) treatment duration. Additionally, the DoVIN2 protein interacted with several enzymes closely associated with sugar metabolism, indicating that DoVIN2 might play a role in abiotic stress responses by regulating the expression of these enzyme genes, thereby enhancing the tolerance of D. officinale to adverse conditions. Conclusions The DoVIN2 gene are involved in various biological processes, including growth and development, stress response, and sugar metabolism. The DoVIN2 might participate in the cold stress response through ABA signaling pathways, while also assuming a negative regulatory function in the response to drought stress. The result provided a basis for further exploring the function of the DoVIN2 gene and a foundation for studying the response of D. officinale to abiotic stresses.
Additional file 1: Table S1. GRAS proteins of litchi, Arabidopsis, and rice. Table S2. Information of LcGRAS genes. Table S3. Syntenic gene pairs among litchi, Arabidopsis and rice. Table S4. Information of miRNA targets in litchi GRAS gene family. Table S5. Gene expression profile of 48 LcGRAS members among four seed development stages (Normalized as FPKM). Table S6. Information of differentially experssed LcGRAS genes. Table S7. Specific primers of 48 LcGRAS genes used for qPCR in this study.
Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi ( Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes ( LcARFs ) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs . Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA- ARF (miRN43- ARF9 ) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E , 7A/7B , 9A/9B , 16A/16B , while a few LcARFs , such as LcARF5A/B , might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.
Sapindaceae is a family of flowering plants, also known as the soapberry family, comprising 141 genera and about 1900 species (Pedro et al., 2010). Most of them are distributed in tropical and subtropical regions, including trees, shrubs, also woody or herbaceous vines. Some are dioecious, while others are monoecious. Many Sapindaceae species possess great economic value; some furnish delicious fruits, like lychee ( Litchi chinensis ), longan ( Dimocarpus longan ), rambutan ( Nephelium lappaceum ); and ackee ( Blighia sapida ) - the national fruit of Jamaica; some produce abundance secondary metabolites, like saponin from soapberry ( Sapindus mukorossi ), and seed oil from yellowhorn ( Xanthoceras sorbifolium ); some yield valuable timber including maple ( Acer spp .) and buckeye ( Aesculus glabra ); and some are of great herbal medicinal value, like balloon-vine ( Cardiospermum halicacabum ). In the last decade, with the rocketing of next generation sequencing (NGS) and genomic technologies, the full genome sequences of several Sapindaceae plants have been resolved (Lin et al., 2017; Liang et al., 2019; Yang et al., 2019; Zhang et al., 2021; Hu et al., 2022; Xue et al., 2022). Among them, our recent publication of the lychee genome attracted broad attention (Edger, 2022; Hu et al., 2022; Lyu, 2022). Now the post-genome era arrives for Sapindaceae, however, there is no public genomic database available for any Sapindaceae species, let alone an integrative database for the whole Sapindaceae family. A unified data platform is in urgent need to collect, manage and share relevant data resources. Therefore, we integrated our home-brew NGS data with all publicly available data for seven Sapindaceae plants and constructed the Sap inaceae Genomic Data Base , named SapBase ( www.sapindaceae.com ), in order to provide genomic resources and an online powerful analytic platform for scientific research on Sapinaceae species and comparative studies with other plants.
OVATE family proteins (OFPs) are a class of plant-specific proteins with a conserved OVATE domain that play fundamental roles in fruit development and plant growth. Mango (
ABSTRACT The Sapindaceae family, encompassing a wide range of plant forms such as herbs, vines, shrubs, and trees, is widely distributed across tropical and subtropical regions. This family includes economically important crops like litchi, longan, rambutan, and ackee. With the wide application of genomic technologies in recent years, several Sapindaceae plant genomes have been decoded, leading to an accumulation of substantial omics data in this field. This surge in data highlights the pressing need for a unified genomic data center capable of storing, sharing, and analyzing these data. Here, we introduced SapBase, that is, the Sapindaceae Genome Database. SapBase houses seven published plant genomes alongside their corresponding gene structure and functional annotations, small RNA annotations, gene expression profiles, gene pathways, and synteny block information. It offers user‐friendly features for gene information mining, co‐expression analysis, and inter‐species comparative genomic analysis. Furthermore, we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in litchi. Thus, SapBase could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.
Many species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position - 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.
Flower development plays vital role in horticultural plants. Post-transcriptional regulation via small RNAs is important for plant flower development. To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour. 'Shixia', an economically important fruit crop in subtropical regions, we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci (PHAS loci), 120 hairpin loci, producing abundant sRNAs, were identified by in-house protocols. Our results suggested that 56 miRNA-target pairs, 22 21-nt-PHAS loci, and 111 hairpin loci are involved in post-transcriptional gene silencing during longan reproductive development. Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled, including miR482-PHAS and miRN15. miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense, and miRN15 is a novel miRNA likely associated with a hairpin locus (HPL-056) to regulate strigolactone receptor gene DWARF14 (D14) and the biogenesis of phasiRNAs from D14. These small RNAs are enriched in flower buds, suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.
In Escherichia coli, acyl carrier protein (ACP) is posttranslationally converted into its active holo-ACP form via covalent linkage of 4′-phosphopantetheine (4′-PP) to residue serine-36. We found that the long flexible 4′-PP arm could react chemoselectively with the iodoacetyl group introduced on solid supports with high efficiency under mild conditions. Based on this finding, we developed site-selective immobilisation of proteins via the active holo-ACP fusion tag, independently of the physicochemical properties of the protein of interest. Furthermore, the molecular ratios of co-immobilised proteins can be manipulated because the tethering process is predominantly directed by the molar concentrations of diverse holo-ACP fusions during co-immobilisation. Conveniently tuning the molecular ratios of co-immobilised proteins allows their cooperation, leading to a highly productive multi-protein co-immobilisation system. Kinetic studies of enzymes demonstrated that α-amylase (Amy) and methyl parathion hydrolase (MPH) immobilised via active tag holo-ACP had higher catalytic efficiency (kcat/Km) in comparison with their corresponding counterparts immobilised via the sulfhydryl groups (-SH) of these proteins. The immobilised holo-ACP-Amy also presented higher thermostability compared with free Amy. The enhanced α-amylase thermostability upon immobilisation via holo-ACP renders it more suitable for industrial application.
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