Search

Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.

Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.

RNA-dependent RNA polymerases (RDRs), involved in the production of various small interfering RNA (siRNA), play critical roles in plant growth, development process, and abiotic/biotic stresses. In this study, 5 RDR genes (AcRDRs) were identified from the pineapple genome. Phylogenetic analysis showed that AcRDRs could be divided into 4 subgroups. Gene structure analysis showed that the number of introns varied from 2 to 18. Furthermore, we analyzed AcRDR expression patterns in vegetative organs and in sexual organs, namely ovules and stamens, at different developmental stages respectively. AcRDR2, AcRDR3 and AcRDR6b showed higher expressions in the male and female reproductive organs, while AcRDR3 also was accumulated highly in sepal and fruit. AcRDR6a exhibited the highest expression levels at the mature ovule and stamen. AcRDR1 had an expression peak in the root. Furthermore, we checked the responses of AcRDRs to abiotic stresses and phytohormones. The results of this study provided basic genomic information for AcRDRs and insights into the probable roles of these genes in plant growth and development.

Pineapple (Ananas comosus L.), a popular tropical fruit, is a good model for evolutionary analysis and genetic research on adaptation to drought habitats, multiple fruits, and crassulacean acid metabolism (CAM) photosynthesis. Reliable reference genes for the normalization of the levels of development-related and/or stress-responsive genes is important for elucidating the mechanisms of plant development as well as their adaptation to various environments. In this study, ten candidate reference genes were selected, and the expression stability of each gene was assessed across 105 pineapple samples, consisting of different reproductive organs (stigma, petal, sepal, ovule, anther, flower, and fruitlet), abiotic stress (salinity, drought, and cold), and hormones (abscisic acid, ethylene, jasmonic acid, and salicylic acid). Our results revealed that PP2A and UBQ were stably expressed during pineapple reproductive development. PP2A and CYC were the stable reference genes across abiotic stress, whereas RAN and EF1α/PP2A was the best candidates for various hormones. To validate the feasibility of using these stably expressed genes for further experiments, we evaluated the expression profile of AcMYB30 across different samples. Our results provide important insights on the growth and development of the pineapple plant as well as information on stress-tolerance genes and stress-signaling pathways in this important fruit.

Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.

Background. As a traditional Chinese medicine, Artemisiae scopariae Herba (ASH) is used to treat various liver diseases. The purpose of this study was to explore the mechanisms of ASH for treating chronic hepatitis B (CHB) using a network pharmacological method. Methods. Bioactive ingredients and related targets of ASH were obtained from Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Gene names of targets were extracted from UniProt database. Differentially expressed genes (DEGs) of CHB were obtained from microarray dataset GSE83148. The intersect genes between DEGs and target genes were annotated using clusterProfiler package. The STRING database was used to obtain a network of protein-protein interactions. Cytoscape 3.7.2 was used to construct the “ingredient-gene-pathway” (IGP) network. Molecular docking studies were performed using Autodock vina. Results. A total of 13 active components were extracted from TCMSP database. Fifteen intersect genes were obtained between 183 target genes and 403 DEGs of GSE83148. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results showed that ASH against CHB mainly involved in toll-like receptor signaling pathway, cellular senescence, hepatitis B, and chemokine signaling pathway. We screened one hub compound, five core targets, and four key pathways from constructed networks. The docking results indicated the strong binding activity between quercetin and AKT1. Conclusions. This study provides potential molecular mechanisms of ASH against CHB based on exploration of network pharmacology.

Background Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored. Results Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response. Conclusions Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants&rsquo, biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress, it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways.

High salinity is one of the major abiotic stresses limiting crops productivity and the geographical distribution of many important crops worldwide. To better understand the salinity stress responses in fiber crop, kenaf (Hibiscus cannabinus L.), a comparative proteomic analysis was performed using the combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser-desorption ionization-time of mass spectrometry (MALDE-TOF/MS), and identified 42 altered protein spots (36 spots were up-represented and 6 down-represented). The majority of these proteins were associated with energy production and metabolism, protein synthesis and degradation, photosynthesis, defense, and reactive oxygen species (ROS) scavenging. A semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) was performed based on peptide sequences for comparing transcript and protein accumulation patterns for 7 candidate proteins. Of these proteins, 5 patterns of induced transcript accumulation were consistent with those of induced protein accumulation. It is possible that the plants proteomic response to salinity stress is a complex signal pathway and that the identified proteins may contribute to facilitating ion homeostasis when plants exposed to salinity stress.

Kenaf (Hibiscus cannabinus), an environmental friendly and economic fiber crop, has a certain tolerance to abiotic stresses. Identification and validation of reliable reference genes for transcript normalization of stress-responsive genes expression by quantitative real-time PCR (qRT-PCR) is important for exploring the molecular mechanisms of plants response to abiotic stresses. In this study, nine candidate reference genes were cloned, and their expression stabilities were assessed in 132 abiotic stress and hormonal stimuli samples of kenaf using geNorm, NormFinder, and BestKeeper algorithms. Results revealed that HcPP2A (Protein phosphatase 2A) and HcACT7 (Actin 7) were the optimum reference genes across all samples; HcUBC (Ubiquitin-conjugating enzyme like protein) was the worst reference gene for transcript normalization. The reliability of the selected reference genes was further confirmed by evaluating the expression profile of HcWRKY28 gene at different stress durations. This work will benefit future studies on discovery of stress-tolerance genes and stress-signaling pathways in this important fiber crop.

In this study, the full-length cDNA of the UDP-glucose pyrophosphorylase gene was isolated from jute by homologous cloning (primers were designed according to the sequence of UGPase gene of other plants) and modified RACE techniques; the cloned gene was designated CcUGPase. Using bioinformatic analysis, the gene was identified as a member of the UGPase gene family. Real-time PCR analysis revealed differential spatial and temporal expression of the CcUGPase gene, with the highest expression levels at 40 and 120 d. PCR and Southern hybridization results indicate that the gene was integrated into the jute genome. Overexpression of CcUGPase gene in jute revealed increased height and cellulose content compared with control lines, although the lignin content remained unchanged. The results indicate that the jute UGPase gene participates in cellulose biosynthesis. These data provide an important basis for the application of the CcUGPase gene in the improvement of jute fiber quality.

Anthracnose, caused by the Colletotrichum species of fungi, is one of the most serious diseases affecting jute in China. The disease causes chlorotic regions with black brown sunken necrotic pits on the surfaces of stems. In late stages of disease, plants undergo defoliation, dieback and blight, which make anthracnose a major threat to jute fiber production and quality in China. In this study, 7 strains of Colletotrichum fungi were isolated from diseased jute stems from Zhejiang, Fujian, Guangxi, and Henan plantations in China. Multi-locus sequence (ACT, TUB2, CAL, GS, GAPDH and ITS) analysis coupled with morphological assessment revealed that C. fructicola, C. siamense and C. corchorum-capsularis sp. nov. were associated with jute anthracnose in southeastern China. C. fructicola and C. siamense were previously not associated with jute anthracnose. C. corchorum-capsularis is a new species formally described here. Pathogenicity tests confirmed that all species can infect jute, causing anthracnose, however the virulence of the 3 species differed. This report is the first associating these three species with jute disease worldwide and is the first description of the pathogens responsible for jute anthracnose in China.

In order to find the correlation between transgelin gene (TAGLN) and colorectal carcinoma occurrence, we investigated the expression of TAGLN in colorectal carcinoma tissue samples and colorectal carcinoma LoVo cells. Meanwhile, the effects of TAGLN on the characteristics of LoVo cells were also examined. The expressions of TAGLN in colorectal carcinoma tissues, adjacent normal tissues, and LoVo cells were detected by the Western blot method. The recombinant plasmid pcDNA3.1-TAGLN was established and transfected into LoVo cells with the help of Lipofectamine™ 2000. At the same time, the TAGLN siRNA was transfected into LoVo cells in another group. Forty-eight hours later, the expressions of TAGLN in all groups were assayed by Western blot, and the cell viability was analyzed by MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. The cell cycle and cell apoptosis were examined by flow cytometry, and the cell invasive ability was analyzed by Transwell invasion experiment. The effect of TALGN on the expression of matrix metalloproteinase 9 (MMP9) was detected by Western blot. Western blot analysis showed that the expressions of TALGN in colorectal carcinoma tissues and LoVo cells were significantly decreased compared with colorectal carcinoma adjacent normal tissues (p < 0.01). In the overexpression or RNAi experiments, the plasmid pcDNA3.1-TAGLN significantly enhanced TALGN expression (p < 0.01), and TAGLN siRNA significantly decreased TAGLN expression (p < 0.01) in LoVo cells 48 h after transfection. In addition, MTT assay indicated that the cell viability of LoVo cells in the pcDNA3.1-TAGLN transfection group was significantly lower than that in the untransfected control group (p < 0.05). Furthermore, the overexpression of TAGLN significantly lowered the cell proliferation index (p < 0.05) and improved cell apoptosis (p < 0.01) in LoVo cells. In Transwell invasive experiments, the cell number, which had migrated through the chamber membrane, significantly decreased in the pcDNA3.1-TAGLN transfection group (p < 0.05) and significantly increased in the TAGLN knockdown group (p < 0.05) compared to the untransfected control group. At the same time, the expression of MMP9 was notably inhibited in the pcDNA3.1-TAGLN transfection group (p < 0.01). The expressions of TAGLN were inhibited in colorectal carcinoma tissues and colorectal carcinoma LoVo cells. The study also demonstrated that TAGLN could attenuate the proliferation and invasive ability of LoVo cells and enhance LoVo cell apoptosis. Furthermore, the expression of MMP9 was also inhibited by TAGLN. All these results could bring us a new perspective for biological therapy in colorectal carcinoma.

Kenaf (Hibiscus cannabinus) is an economic and ecological fiber crop but suffers severe losses in fiber yield and quality under the stressful conditions of excess salinity and drought. To explore the mechanisms by which kenaf responds to excess salinity and drought, gene expression was performed at the transcriptomic level using RNA-seq. Thus, it is crucial to have a suitable set of reference genes to normalize target gene expression in kenaf under different conditions using real-time quantitative reverse transcription-PCR (qRT-PCR). In this study, we selected 10 candidate reference genes from the kenaf transcriptome and assessed their expression stabilities by qRT-PCR in 14 NaCl- and PEG-treated samples using geNorm, NormFinder, and BestKeeper. The results indicated thatTUBαand 18S rRNA were the optimum reference genes under conditions of excess salinity and drought in kenaf. Moreover,TUBαand 18S rRNA were used singly or in combination as reference genes to validate the expression levels of WRKY28 and WRKY32 in NaCl- and PEG-treated samples by qRT-PCR. The results further proved the reliability of the two selected reference genes. This work will benefit future studies on gene expression and lead to a better understanding of responses to excess salinity and drought in kenaf.

The Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a key enzyme in lignin biosynthesis in plants. In this study we cloned the full-length cDNA of the Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene from jute using homology clone (primers were designed according to the sequence of CCoAOMT gene of other plants), and a modified RACE technique, subsequently named "CcCCoAOMT1". Bioinformatic analyses showed that the gene is a member of the CCoAOMT gene family. Real-time PCR analysis revealed that the CcCCoAOMT1 gene is constitutively expressed in all tissues, and the expression level was greatest in stem, followed by stem bark, roots and leaves. In order to understand this gene's function, we transformed it into Arabidopsis thaliana; integration (one insertion site) was confirmed following PCR and southern hybridization. The over-expression of CcCCoAOMT1 in these transgenic A.thaliana plants resulted in increased plant height and silique length relative to non-transgenic plants. Perhaps the most important finding was that the transgenic Arabidopsis plants contained more lignin (20.44-21.26%) than did control plants (17.56%), clearly suggesting an important role of CcCCoAOMT1 gene in lignin biosynthesis. These data are important for the success of efforts to reduce jute lignin content (thereby increasing fiber quality) via CcCCoAOMT1 gene inhibition.