Aim： To determine the possible roles of the t-complex testis expressed gene 5 （Tctex5） on sperm functions, the fulllength sequence of mRNA was studied and compared in the testis between the normal wild-type and the...Aim： To determine the possible roles of the t-complex testis expressed gene 5 （Tctex5） on sperm functions, the fulllength sequence of mRNA was studied and compared in the testis between the normal wild-type and the sterile t-haplotype mutant mice. Methods： We applied rapid amplification of cDNA ends, Northern blot and reverse transcription polymerase chain reaction to analyze the full length of Tctex5 mRNAs isolated from testes of the wild-type and the t-haplotype mice. Reverse transcription polymerase chain reaction was used to semi-quantitatively compare expression of Tctex5 transcripts in the 16 tissues and 9.5 day stage embryos in the wild-type mice. E-translation was applied to estimate the amino acid sequences. Results： One long and one short transcript of Tctex5 mRNA were discovered in mouse testis of wild-type （Tctex5^long-＋ and Tctex5^short-＋） and t-haplotype （Tctex5^long-＋ and Tctex5^short-＋） mice, respectively. Being enhanced only in the testis, Tctex5^long-＋ had 17 point mutations and one 15-bp-deletion in the exon 1 region, comparing with the Tctex5^long-＋, whereas the Tctex5^short-＋ was similar to the Tctex5^short-＋. The short isoforms of Tctex5 mRNAs in the two models encoded exactly the same peptides, but the long isoforms did not. The estimated peptide encoded by Tctex5^long-＋ had significant mutations on putative sites of phosphorylation and PP1 binding. Conclusion： We established that mutations that occur in the Tctex5 long transcript of the t-haplotype mice are important for normal sperm function, whereas the short transcript of Tctex5 might have a conserved function among different tissues. （Asian J Androl 2008 Mar; 10： 219-226）展开更多
Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has bee...Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research,molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii.This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii.As a result,123 ApAP2/ERFs were obtained.Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies.The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their chromosomal locations,conserved proteinmotifs,and gene duplication events.Moreover,investigating gene promoters revealed their potential involvement in developmental regulation,physiological processes,and stress adaptationmechanisms.Measurements of anthocyanin content revealed a notable increase in red leaves during autumn.Utilizing transcriptome data,transcriptomic profiling revealed that the majority of AP2/ERF genes in Acer paxii displayed significant differential expression between red and green leaves during the color-changing period.Furthermore,through qRT-PCR analysis,it was found that the gene expression levels of ApERF006,ApERF014,ApERF048,ApERF097,and ApERF107 were significantly elevated in red leaves.This indicates their potential participation in leaf pigmentation processes.These findings offer significant insights into the biological significance of ApAP2/ERF transcription factors and lay the groundwork for subsequent investigations into their regulatorymechanisms underlying leaf pigmentation in Acer paxii.展开更多
The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic ...The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic bioinformatics and functional studies in this species.A total of 33 SmBBX genes were identified through genome-wide analysis.These genes were phylogenetically grouped into five major clades,with shared domain structures,motifs,and genomic architectures among clade members.The gene duplication analysis revealed segmental duplication as the primary mechanism underlying the expansion of SmBBX proteins in eggplant.Additionally,expression profiling across diverse tissues and abiotic stress conditions,combined with the construction of protein—protein interaction networks and luciferase complementation assay,provided valuable insights into the functional roles of SmBBX genes.SmBBX21-2 and SmBBX22 were identified as the key regulators of anthocyanin biosynthesis,activating the expression of SmCHS and SmDFR promoters.Functional validation via heterologous and homologous overexpression demonstrated that SmBBX22 promoted anthocyanin accumulation by upregulating the expression of structural genes(SmCHS,SmF3H,SmF3′5′H,SmDFR,and SmANS)and transcription factors(SmTT8 and SmHY5)important for anthocyanin biosynthesis.Furthermore,the integration of DNA affinity purification sequencing and RNA-seq data revealed the direct transcriptional targets of SmBBX22,including genes involved in secondary metabolism,hormone signaling,and developmental regulation.This highlighted the role of SmBBX22 in phenylpropanoid and flavonoid biosynthesis.This study lays the foundation for understanding the functional roles of BBX genes in eggplant and provides new directions for future research in plant metabolism and stress adaptation.展开更多
Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA...Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.展开更多
The prognosis for patients who experience intracerebral hemorrhage is poor because of a lack of effective treatments.Tumor necrosis factor-α-stimulated gene 6(TSG6)is a secreted glycoprotein that exerts anti-inflamma...The prognosis for patients who experience intracerebral hemorrhage is poor because of a lack of effective treatments.Tumor necrosis factor-α-stimulated gene 6(TSG6)is a secreted glycoprotein that exerts anti-inflammatory effects in various inflammatory diseases.We previously showed that adipose-derived stem cells can inhibit inflammation by upregulating TSG6 secretion in an in vitro model of intracerebral hemorrhage.However,the direct effects of TSG6 on hematoma clearance in vivo remain largely unknown.The aim of this study was to determine how TSG6 affects hematoma absorption in mice subjected to intracerebral hemorrhage and to explore the potential underlying mechanisms.We first analyzed the gene profiles of patients with intracerebral hemorrhage from the GEO database and examined changes in TSG6 expression in the brain tissues of mice subjected to intracerebral hemorrhage.We found that TSG6 expression exhibited a transient increase following intracerebral hemorrhage,and that there was a negative correlation between the initial hematoma volume and TSG6 levels.Immunofluorescence analysis showed that TSG6 was primarily expressed in microglia and macrophages.Furthermore,we found that TSG6 promoted functional recovery in mice subjected to intracerebral hemorrhage by accelerating hematoma clearance,reducing the number of apoptotic cells and degenerated neurons,increasing the proportion of phagocytic microglia/macrophages,and decreasing iron deposition.Western blotting and immunofluorescence analysis indicated that TSG6 promoted M2 polarization of microglia/macrophages.In vitro phagocytosis experiments confirmed that TSG6 enhanced the ability of microglia to phagocytize red blood cells.Finally,we identified the signal transducer and activator of transcription 6/growth arrest-specific protein 6 signaling pathway as playing a critical role in TSG6-mediated hematoma absorption.In summary,our results demonstrate an essential role for TSG6 in promoting hematoma absorption in a mouse model of intracerebral hemorrhage.These findings suggest that TSG6 accelerates hematoma clearance and improves neurological function by promoting microglia/macrophage polarization to the M2 phenotype,activating the STAT6/GAS6 signaling pathway,and increasing phagocytic receptor expression on the surface of phagocytes,thereby enhancing their ability to phagocytize red blood cells.展开更多
Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revea...Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCα CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atpl, cox1, cox2, cob, rm5S, and rm26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F1, but no transcript was detected in floral buds of the maintainer line.The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F1. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.展开更多
Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,p...Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,post transcriptional gene silencing.At the moment,people have mainly focused on the study of post transcriptional gene silencing and found its features:extensivity,conduction and peculiarity,also put forward some hypothesis for its mechanisms,for example,RNA threshold model,aberrant RNA model,inter or intra molecular base pairing model and so on.Furthermore,post transcriptional gene silencing is being applied in gene engineering of plants.Recently the people have found that post transcriptional gene silencing has bearing on capacity plants resisting virus.Many researchers have studied post transcriptional gene silencing,but there are some questions which need be solved in the future.This article summarizes progresses in features,mechanisms,applies of post transcriptional gene silencing about transgenic plants.展开更多
[Objective] Cloning of the AtrMYB transcription factor gene from Acer truncatum was conducted to further explore the red leaf development mechanism and breed cultivars of colored-leaf maple. [Method] The Acer truncat...[Objective] Cloning of the AtrMYB transcription factor gene from Acer truncatum was conducted to further explore the red leaf development mechanism and breed cultivars of colored-leaf maple. [Method] The Acer truncatum ‘Luhong No.1＇ cultivar was used as the material for cloning the MYB gene by mean of RTPCR and RACE-PCR. [Results] Sequence analysis showed that the fragment contained a full coding region of 831 bp encoding 276 amino acid residues with a molecular weight of 32.17 kD and a molecular formula C_（1430）H_（14052）N_（2247）O_（406）S_（14）. The gene was named as AtrMYB with a Gen Bank accession number of 1825712. This coded protein had apI of 9.44. The results showed that the AtrMYB exhibited typical features of the R2R3-MYB domain. The AtrMYB was highly homologous with the MYB of other species at nucleotide and amino acid levels. The AtrMYB had no signal peptide, but a nuclear localization signal. The phylogenetic tree showed that the AtrMYB was at the same clade as the MYB from Citrus sinensis. [Conclusion] The AtrMYB was cloned from Acer truncatum ‘Luhong No.1＇ cultivar. These results have provided a foundation for further purification and identification of target protein and function study of the AtrMYB.展开更多
Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a mu...Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes.展开更多
Based on sequencing of part clones in a root subtractive cDNA library, an expressed sequence tag （EST） sharing high similarity to a rice C2H2 zinc finger transcription factor （ZFP15） was obtained in wheat. Through...Based on sequencing of part clones in a root subtractive cDNA library, an expressed sequence tag （EST） sharing high similarity to a rice C2H2 zinc finger transcription factor （ZFP15） was obtained in wheat. Through bioinformatics approach, the wheat C2H2-type ZFP gene referred to TaZFP15 has been identified and characterized. As a full-length cDNA of 670 bp, TaZFP15 has an open reading frame of 408 bp and encodes a 135-aa polypeptide. TaZFP15 contains two C2H2 zinc finger domains and each one has a conserved motif QALGGH. The typical L-box, generally identified in the C2H2 type transcription factors, has also been found in TaZFP15. Phylogenetic analysis suggested that TaZFP15 shares high similarities with rice ZFP15 （GenBank accession no. AY286473）, maize ZFP （GenBank accession no. NM_001159094） and a subset of other zinc-finger transcription factor genes in plant species. The expression of TaZFP15 was up-regulated by starved-Pi stress, showing a pattern to be gradually elevated along with the progression of the Pi-stress in a 23-h treatment regime. Similarly, the transcripts of TaZFP15 in roots were also induced by nitrogen deficiency, and abiotic stresses of drought and salinity. No responses of TaZFP15 were detected in roots to nutrition deficiencies of P, Zn, and Ca, and the external treatment of abscisic acid （ABA）. TaZFP15 could be specifically amplified in genome A, B, and D, and without variability in the sequences, suggesting that TaZFP15 has multi-copies in the homologous hexaploid species. Transgenic analysis in tobacco revealed that up-regulation of TaZFP15 could significantly improve plant dry mass accumulation via increasing the plant phosphorus acquisition capacity under Pi-deficiency condition. The results suggested that TaZFP15 is involved in mediation of signal transductions of diverse external stresses.展开更多
Zinc finger-homeodomain proteins(ZF-HDs) are transcription factors that regulate plant growth,development,and abiotic stress tolerance.The SL-ZH13 gene was found to be significantly upregulated under drought stress tr...Zinc finger-homeodomain proteins(ZF-HDs) are transcription factors that regulate plant growth,development,and abiotic stress tolerance.The SL-ZH13 gene was found to be significantly upregulated under drought stress treatment in tomato(Solanum lycopersicum) leaves in our previous study.In this study,to further understand the role that the SL-ZH13 gene plays in the response of tomato plants to drought stress,the virus-induced gene silencing(VIGS) method was applied to downregulate SL-ZH13 expression in tomato plants,and these plants were treated with drought stress to analyze the changes in drought tolerance.The SL-ZH13 silencing efficiency was confirmed by quantitative real-time PCR(qRT-PCR) analysis.In SL-ZH13-silenced plants,the stems wilted faster,leaf shrinkage was more severe than in control plants under the same drought stress treatment conditions,and the mean stem bending angle of SL-ZH13-silenced plants was smaller than that of control plants.Physiological analyses showed that the activity of superoxide dismutase(SOD) and peroxidase(POD) and the content of proline(Pro) in SL-ZH13-silenced plants were lower than those in control plants after 1.5 and 3 h of drought stress treatment.The malondialdehyde(MDA) content in SL-ZH13-silenced plants was higher than that in control plants after 1.5 and 3 h of drought stress treatment,and H2O2 and O2^-· accumulated much more in the leaves of SL-ZH13-silenced plants than in the leaves of control plants.These results suggested that silencing the SL-ZH13 gene affected the response of tomato plants to drought stress and decreased the drought tolerance of tomato plants.展开更多
To investigate whether transcription of hepatitis B virus （HBV） gene occurs in human sperm, total RNA was extracted from sperm of patients with chronic HBV infection （test-I）, from donor sperm transfected with a p...To investigate whether transcription of hepatitis B virus （HBV） gene occurs in human sperm, total RNA was extracted from sperm of patients with chronic HBV infection （test-I）, from donor sperm transfected with a plasmid containing the full-length HBV genome （test-2）, and from nontransfected donor sperm （control）, used as the template for reverse transcription-polymerase chain reaction （RT-PCR）. Positive bands for HBV DNA were observed in the test groups but not in the control. Next, to identify the role of host genes in regulating viral gene transcription in sperm, total RNA was extracted from 2-cell embryos derived from hamster oocytes fertilized in vitro by HBV-transfected （test） or nontransfected （control） human sperm and successively subjected to SMART-PCR, suppression subtractive hybridization, T/A cloning, bacterial amplification, microarray hybridization, sequencing and the Basic Local Alignment Search Tool （BLAST） search to isolate differentially expressed genes. Twenty-nine sequences showing significant identity to five human gene families were identified, with chorionic somatomammotropin hormone 2 （CSH2）, eukaryotic translation initiation factor 4 gamma 2 （EIF4G2）, pterin-4 alpha-carbinolamine dehydratase 2 （PCBD2）, pregnancy-specific beta-l-glycoprotein 4 （PSG4） and titin （TTN） selected to represent target genes. Using real-time quantitative RT-PCR （qRT-PCR）, when CSH2 and PCBD2 （or EIF4G2, PSG4 and TTN） were silenced by RNA interference, transcriptional levels of HBV s and x genes significantly decreased （or increased） （P 〈 0.05）. Silencing of a control gene in sperm did not significantly change transcription of HBV s and x genes （P 〉 0.05）. This study provides the first experimental evidence that transcription of HBV genes occurs in human sperm and is regulated by host genes.展开更多
WRKY transcription factors are involved in the regulation of response to biotic and abiotic stresses in plants. A full-length cDNA clone of rice WRKY82 gene （OsWRKY82） was isolated from a cDNA library generated from...WRKY transcription factors are involved in the regulation of response to biotic and abiotic stresses in plants. A full-length cDNA clone of rice WRKY82 gene （OsWRKY82） was isolated from a cDNA library generated from leaves infected by Magnaporthe grisea. OsWRKY82 contained an entire open reading frame in length of 1 701 bp, and was predicted to encode a polypeptide of 566 amino acid residues consisting of two WRKY domains, each with a zinc finger motif of C2H2, belonging to the WRKY subgroup I. OsWRKY82 shared high identity at the amino acid level with those from Sorghum bicolor, Hordeum vulgare, and Zea mays. The transcript level of OsWRKY82 was relatively higher in stems, leaves, and flowers, and less abundant in grains. It was induced by inoculation with M. grisea and Rhizoctonia solani. However, the inducible expression in incompatible rice-M. grisea interactions was earlier and greater than that in compatible interactions. The expression of OsWRKY82 was up-regulated by methyl jasmonate and ethephon, whereas salicylic acid exerted no effects on its expression. Moreover, OsWRKY82 exhibited transcriptional activation ability in yeast. Additionally, OsWRKY82 transcripts could be induced by wounding and heat shocking, but not by abscisic acid, cold, high salinity and dehydration. By contrast, gibberellin suppressed the expression of OsWRKY82. These indicate that OsWRKY82 is a multiply stress-inducible gene responding to both biotic and abiotic stresses, and may be involved in the regulation of defense response to pathogens and tolerance against abiotic stresses by jasmonic acid/ethylene-dependent signaling pathway.展开更多
The human RNA methyltransferase like i gene(RNMTL1)is one of thirteen newly discovered geneswithin a 116 Kb segment of the chromosome 17p13.3 that suffers from a high frequent loss of heterozygosityin human hepatocell...The human RNA methyltransferase like i gene(RNMTL1)is one of thirteen newly discovered geneswithin a 116 Kb segment of the chromosome 17p13.3 that suffers from a high frequent loss of heterozygosityin human hepatocellular carcinoma in China[1-5].To understand the molecular mechanisms underlyingtranscription control of the RNMTL1 gene in human cancers,we decline using of the conventional approachwhere the cis-elements bound by the known transcription factors are primary targets,and carried out thesystematic analyses to dissect the promoter structure and identify/characterize the key cis-elements thatare responsible for its strong expression in cell.The molecular approaches applied included 1,the primerextension for mapping of the transcription starts;2,the transient transfection/reporter assays on a largenumber of deletion and site-specific mutants of the promoter segment for defining the minimal promoterand the crucial elements within;and 3,the electrophoresis mobility shift assay with specific antibodies forreconfirming the nature of the transcription factors and their cognate cis-elements.We have shown that theinteraction of an ATF/CREB element(-38 to-31)and its cognate transcription factors play a predominantrole in the promoter activity of the RNMTL1 gene.The secondary DNA structures of the ATF/CREBelement play a more vital role in the protein-DNA interaction.Finally,we reported a novel mechanismunderlying the YY1 mediated transcription repression,namely,the ATF/CREB dependent transcription-repression by YY1 is executed in absence of its own sequence-specific binding.展开更多
Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription fact...Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription factors play important regulatory roles in growth, development,dormancy and abiotic stress. To date, bZIP transcription factors have not been systematically studied in P. mume. In this study, 49 bZIP genes were first identified in P. mume, and the PmbZIP family was divided into 12 groups according to the grouping principles for the Arabidopsis thaliana bZIP family. For the first time, we constructed a detailed model of the PmbZIP domains(R-x_(3)–N-(x)_7-R/K-x_(2)-K-x_(6)-L-x_(6)-L-_(6)-L). Phylogenetic and synteny analyses showed that PmbZIPs duplication events might have occurred during the large-scale genome duplication events. A relatively short time of speciation and the finding that 91.84% of the bZIP genes formed orthologous pairs between P. mume and Prunus armeniaca provided evidence of a close relationship. Gene expression patterns were analysed in different tissues and periods, indicating that PmbZIP genes with the same motifs exhibited similar expression patterns. The gene expression results showed that PmbZIP31/36/41 genes played a more prominent role in the response to freezing stress than cold stress. The expression level of almost all subset Ⅲ genes was upregulated under freezing treatment, especially after cold exposure. We analysed the gene expression patterns of PmbZIP12/31/36/41/48 and their responses to low-temperature stress, which provided useful resources for future studies on the cold/freezing-tolerant molecular breeding of P. mume.展开更多
Axon regeneration is crucial for recovery from neurological diseases. Numerous studies have identified several genes, microRNAs （miRNAs）, and transcription factors （TFs） that influence axon regeneration. However, ...Axon regeneration is crucial for recovery from neurological diseases. Numerous studies have identified several genes, microRNAs （miRNAs）, and transcription factors （TFs） that influence axon regeneration. However, the regulatory networks involved have not been fully elucidated. In the present study, we analyzed a regulatory network of 51 miRNAs, 27 TFs, and 59 target genes, which is involved in axon regeneration. We identified 359 pairs of feed- forward loops （FFLs）, seven important genes （Naplll, Arhgef12, Sema6d, Akt3, Trim2, Rabllfip2, and Rps6ka3）, six important miRNAs （hsa-miR-204-5p, hsa-miR-124-3p, hsa-miR-26a-5p, hsa-miR-16-5p, hsa-miR-17-5p, and hsa- miR-15b-5p）, and eight important TFs （Smada2, Flil, Wtl, Sp6, Sp3, Smad4, Smad5, and Crebl）, which appear to play an important role in axon regeneration. Functional enrichment analysis revealed that axon-associated genes are involved mainly in the regulation of cellular component organization, axonogenesis, and cell morphogenesis during neuronal differentiation. However, these findings need to be validated by further studies.展开更多
Saccharina japonica is a common macroalga in sublittoral communities of cold seawater environments, and consequently may have highly efficient ribulose-1, 5-bisphosphate carboxylase/ oxygenase （Rubisco） activity for...Saccharina japonica is a common macroalga in sublittoral communities of cold seawater environments, and consequently may have highly efficient ribulose-1, 5-bisphosphate carboxylase/ oxygenase （Rubisco） activity for carbon assimilation. In our study, we cloned the full-length Rubisco gene from S.japonica （SJ-rbc）. It contained an open reading frame for a large subunit gene （SJ-rbcL） of 1 467 bp, a small subunit gene （SJ-rbcS） of 420 bp, and a SJ-rbcL/S intergenie spacer of 269 bp. The deduced peptides of SJ-rbcL and SJ-rbcS were 488 and 139 amino acids with theoretical molecular weights and isoelectric points of 53.97 kDa, 5.81 and 15,84 kDa, 4.71, respectively. After induction with 1 mmol/L isopropyl-β-D- thiogalactopyranoside for 5 h and purification by Ni2＋ affinity chromatography, electrophoresis and western blot detection demonstrated successful expression of the 55 kDa SJ-rbcL protein. Real-time quantitative PCR showed that the mRNA levels of SJ-rbcL in gametophytes increased when transferred into normal growth conditions and exhibited diurnal variations： increased expression during the day but suppressed expression at night. This observation implied that Rubisco played a role in normal gametophytic growth and development. In juvenile sporophytes, mRNA levels of SJ-rbcL, carbonic anhydrase, Calvin-Benson- Bassham cycle-related enzyme, and chloroplast light-harvesting protein were remarkably increased under continuous light irradiance. Similarly, expression of these genes was up-regulated under blue light irradiance at 350 umol/（m2.s）. Our results indicate that long-term white light and short-term blue light irradiance enhances juvenile sporophytic growth by synergistic effects of various photosynthetic elements.展开更多
Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 f...Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.展开更多
This paper investigates the stochastic resonance （SR） induced by a multiplicative periodic signal in the gene transcriptional regulatory system with correlated noises. The expression of the signal-to-noise ratio （...This paper investigates the stochastic resonance （SR） induced by a multiplicative periodic signal in the gene transcriptional regulatory system with correlated noises. The expression of the signal-to-noise ratio （SNR） is derived. The results indicate that the existence of a maximum in SNR vs. the additive noise intensity α the multiplicative noise intensity D and the cross-correlated noise intensity λ is the identifying characteristic of the SR phenomenon and there is a critical phenomenon in the SNR as a function of λ, i.e., for the case of smaller values of noise intensity （α or D）, the SNR decreases as λ increases; however, for the case of larger values of noise intensity （α or D）, the SNR increases as λ increases.展开更多
文摘Aim： To determine the possible roles of the t-complex testis expressed gene 5 （Tctex5） on sperm functions, the fulllength sequence of mRNA was studied and compared in the testis between the normal wild-type and the sterile t-haplotype mutant mice. Methods： We applied rapid amplification of cDNA ends, Northern blot and reverse transcription polymerase chain reaction to analyze the full length of Tctex5 mRNAs isolated from testes of the wild-type and the t-haplotype mice. Reverse transcription polymerase chain reaction was used to semi-quantitatively compare expression of Tctex5 transcripts in the 16 tissues and 9.5 day stage embryos in the wild-type mice. E-translation was applied to estimate the amino acid sequences. Results： One long and one short transcript of Tctex5 mRNA were discovered in mouse testis of wild-type （Tctex5^long-＋ and Tctex5^short-＋） and t-haplotype （Tctex5^long-＋ and Tctex5^short-＋） mice, respectively. Being enhanced only in the testis, Tctex5^long-＋ had 17 point mutations and one 15-bp-deletion in the exon 1 region, comparing with the Tctex5^long-＋, whereas the Tctex5^short-＋ was similar to the Tctex5^short-＋. The short isoforms of Tctex5 mRNAs in the two models encoded exactly the same peptides, but the long isoforms did not. The estimated peptide encoded by Tctex5^long-＋ had significant mutations on putative sites of phosphorylation and PP1 binding. Conclusion： We established that mutations that occur in the Tctex5 long transcript of the t-haplotype mice are important for normal sperm function, whereas the short transcript of Tctex5 might have a conserved function among different tissues. （Asian J Androl 2008 Mar; 10： 219-226）
基金supported by the National Natural Science Foundation of China[grant numbers 32271914 and 32301660]the Quality Engineering Project of Anhui Provincial Department of Education[grant number 2023zygzts007].
文摘Acer paxii belongs to the evergreen species of Acer,but it exhibits a unique feature of reddish leaves in fall in subtropical regions.Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research,molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii.This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii.As a result,123 ApAP2/ERFs were obtained.Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies.The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their chromosomal locations,conserved proteinmotifs,and gene duplication events.Moreover,investigating gene promoters revealed their potential involvement in developmental regulation,physiological processes,and stress adaptationmechanisms.Measurements of anthocyanin content revealed a notable increase in red leaves during autumn.Utilizing transcriptome data,transcriptomic profiling revealed that the majority of AP2/ERF genes in Acer paxii displayed significant differential expression between red and green leaves during the color-changing period.Furthermore,through qRT-PCR analysis,it was found that the gene expression levels of ApERF006,ApERF014,ApERF048,ApERF097,and ApERF107 were significantly elevated in red leaves.This indicates their potential participation in leaf pigmentation processes.These findings offer significant insights into the biological significance of ApAP2/ERF transcription factors and lay the groundwork for subsequent investigations into their regulatorymechanisms underlying leaf pigmentation in Acer paxii.
基金supported by grants from Shanghai Agriculture Applied Technology Development Program(Grant No.2022-02-08-00-12-F01109)the National Natural Science Foundation of China(Grant No.32272721).
文摘The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic bioinformatics and functional studies in this species.A total of 33 SmBBX genes were identified through genome-wide analysis.These genes were phylogenetically grouped into five major clades,with shared domain structures,motifs,and genomic architectures among clade members.The gene duplication analysis revealed segmental duplication as the primary mechanism underlying the expansion of SmBBX proteins in eggplant.Additionally,expression profiling across diverse tissues and abiotic stress conditions,combined with the construction of protein—protein interaction networks and luciferase complementation assay,provided valuable insights into the functional roles of SmBBX genes.SmBBX21-2 and SmBBX22 were identified as the key regulators of anthocyanin biosynthesis,activating the expression of SmCHS and SmDFR promoters.Functional validation via heterologous and homologous overexpression demonstrated that SmBBX22 promoted anthocyanin accumulation by upregulating the expression of structural genes(SmCHS,SmF3H,SmF3′5′H,SmDFR,and SmANS)and transcription factors(SmTT8 and SmHY5)important for anthocyanin biosynthesis.Furthermore,the integration of DNA affinity purification sequencing and RNA-seq data revealed the direct transcriptional targets of SmBBX22,including genes involved in secondary metabolism,hormone signaling,and developmental regulation.This highlighted the role of SmBBX22 in phenylpropanoid and flavonoid biosynthesis.This study lays the foundation for understanding the functional roles of BBX genes in eggplant and provides new directions for future research in plant metabolism and stress adaptation.
文摘Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers of spinal cord injury.
基金supported by the National Natural Science Foundation of China,Nos.92148206,82071330(both to ZT),82201474(to GL)a grant from Tongji Hospital,No.2022ZHFY01(to ZT).
文摘The prognosis for patients who experience intracerebral hemorrhage is poor because of a lack of effective treatments.Tumor necrosis factor-α-stimulated gene 6(TSG6)is a secreted glycoprotein that exerts anti-inflammatory effects in various inflammatory diseases.We previously showed that adipose-derived stem cells can inhibit inflammation by upregulating TSG6 secretion in an in vitro model of intracerebral hemorrhage.However,the direct effects of TSG6 on hematoma clearance in vivo remain largely unknown.The aim of this study was to determine how TSG6 affects hematoma absorption in mice subjected to intracerebral hemorrhage and to explore the potential underlying mechanisms.We first analyzed the gene profiles of patients with intracerebral hemorrhage from the GEO database and examined changes in TSG6 expression in the brain tissues of mice subjected to intracerebral hemorrhage.We found that TSG6 expression exhibited a transient increase following intracerebral hemorrhage,and that there was a negative correlation between the initial hematoma volume and TSG6 levels.Immunofluorescence analysis showed that TSG6 was primarily expressed in microglia and macrophages.Furthermore,we found that TSG6 promoted functional recovery in mice subjected to intracerebral hemorrhage by accelerating hematoma clearance,reducing the number of apoptotic cells and degenerated neurons,increasing the proportion of phagocytic microglia/macrophages,and decreasing iron deposition.Western blotting and immunofluorescence analysis indicated that TSG6 promoted M2 polarization of microglia/macrophages.In vitro phagocytosis experiments confirmed that TSG6 enhanced the ability of microglia to phagocytize red blood cells.Finally,we identified the signal transducer and activator of transcription 6/growth arrest-specific protein 6 signaling pathway as playing a critical role in TSG6-mediated hematoma absorption.In summary,our results demonstrate an essential role for TSG6 in promoting hematoma absorption in a mouse model of intracerebral hemorrhage.These findings suggest that TSG6 accelerates hematoma clearance and improves neurological function by promoting microglia/macrophage polarization to the M2 phenotype,activating the STAT6/GAS6 signaling pathway,and increasing phagocytic receptor expression on the surface of phagocytes,thereby enhancing their ability to phagocytize red blood cells.
基金This work was supported by the National High Technology R&D Project of China (No.2002AA207009) and Wuhan Dawn Project for Youth (No. 20035002016-36).
文摘Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCα CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atpl, cox1, cox2, cob, rm5S, and rm26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F1, but no transcript was detected in floral buds of the maintainer line.The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F1. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.
文摘Since transgene silencing was found in transgenic plants,many scholars have studied it extensively and considered that it has three functional mechanisms:post dependent gene silencing,transcriptional gene silencing,post transcriptional gene silencing.At the moment,people have mainly focused on the study of post transcriptional gene silencing and found its features:extensivity,conduction and peculiarity,also put forward some hypothesis for its mechanisms,for example,RNA threshold model,aberrant RNA model,inter or intra molecular base pairing model and so on.Furthermore,post transcriptional gene silencing is being applied in gene engineering of plants.Recently the people have found that post transcriptional gene silencing has bearing on capacity plants resisting virus.Many researchers have studied post transcriptional gene silencing,but there are some questions which need be solved in the future.This article summarizes progresses in features,mechanisms,applies of post transcriptional gene silencing about transgenic plants.
基金Supported by Agricultural Elite Cultivar Project of Shandong Province(lkz2014[96])~~
文摘[Objective] Cloning of the AtrMYB transcription factor gene from Acer truncatum was conducted to further explore the red leaf development mechanism and breed cultivars of colored-leaf maple. [Method] The Acer truncatum ‘Luhong No.1＇ cultivar was used as the material for cloning the MYB gene by mean of RTPCR and RACE-PCR. [Results] Sequence analysis showed that the fragment contained a full coding region of 831 bp encoding 276 amino acid residues with a molecular weight of 32.17 kD and a molecular formula C_（1430）H_（14052）N_（2247）O_（406）S_（14）. The gene was named as AtrMYB with a Gen Bank accession number of 1825712. This coded protein had apI of 9.44. The results showed that the AtrMYB exhibited typical features of the R2R3-MYB domain. The AtrMYB was highly homologous with the MYB of other species at nucleotide and amino acid levels. The AtrMYB had no signal peptide, but a nuclear localization signal. The phylogenetic tree showed that the AtrMYB was at the same clade as the MYB from Citrus sinensis. [Conclusion] The AtrMYB was cloned from Acer truncatum ‘Luhong No.1＇ cultivar. These results have provided a foundation for further purification and identification of target protein and function study of the AtrMYB.
基金funded by the Biotechnology and Biological Sciences Research Council(BBSRC) ERA-NET BB/G024995/1
文摘Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes.
基金supported by the National Natural Science Foundation of China (30971773)the Natural Science Foundation of Hebei Province,China (C2011204031)the Key Laboratory of Crop Growth Regulation of Hebei Province,China
文摘Based on sequencing of part clones in a root subtractive cDNA library, an expressed sequence tag （EST） sharing high similarity to a rice C2H2 zinc finger transcription factor （ZFP15） was obtained in wheat. Through bioinformatics approach, the wheat C2H2-type ZFP gene referred to TaZFP15 has been identified and characterized. As a full-length cDNA of 670 bp, TaZFP15 has an open reading frame of 408 bp and encodes a 135-aa polypeptide. TaZFP15 contains two C2H2 zinc finger domains and each one has a conserved motif QALGGH. The typical L-box, generally identified in the C2H2 type transcription factors, has also been found in TaZFP15. Phylogenetic analysis suggested that TaZFP15 shares high similarities with rice ZFP15 （GenBank accession no. AY286473）, maize ZFP （GenBank accession no. NM_001159094） and a subset of other zinc-finger transcription factor genes in plant species. The expression of TaZFP15 was up-regulated by starved-Pi stress, showing a pattern to be gradually elevated along with the progression of the Pi-stress in a 23-h treatment regime. Similarly, the transcripts of TaZFP15 in roots were also induced by nitrogen deficiency, and abiotic stresses of drought and salinity. No responses of TaZFP15 were detected in roots to nutrition deficiencies of P, Zn, and Ca, and the external treatment of abscisic acid （ABA）. TaZFP15 could be specifically amplified in genome A, B, and D, and without variability in the sequences, suggesting that TaZFP15 has multi-copies in the homologous hexaploid species. Transgenic analysis in tobacco revealed that up-regulation of TaZFP15 could significantly improve plant dry mass accumulation via increasing the plant phosphorus acquisition capacity under Pi-deficiency condition. The results suggested that TaZFP15 is involved in mediation of signal transductions of diverse external stresses.
基金supported by the earmarked fund for China Agriculture Research System(CARS-25-A-15)the Breeding of New Staple Vegetable Varieties of Heilongjiang Province,China(GA15B103)+2 种基金the Natural Science Foundation of Heilongjiang Province,China(C2017024)the Youth Talent Support Program of Northeast Agricultural University,China(17QC07)the National Natural Science Foundation of China(31501777)
文摘Zinc finger-homeodomain proteins(ZF-HDs) are transcription factors that regulate plant growth,development,and abiotic stress tolerance.The SL-ZH13 gene was found to be significantly upregulated under drought stress treatment in tomato(Solanum lycopersicum) leaves in our previous study.In this study,to further understand the role that the SL-ZH13 gene plays in the response of tomato plants to drought stress,the virus-induced gene silencing(VIGS) method was applied to downregulate SL-ZH13 expression in tomato plants,and these plants were treated with drought stress to analyze the changes in drought tolerance.The SL-ZH13 silencing efficiency was confirmed by quantitative real-time PCR(qRT-PCR) analysis.In SL-ZH13-silenced plants,the stems wilted faster,leaf shrinkage was more severe than in control plants under the same drought stress treatment conditions,and the mean stem bending angle of SL-ZH13-silenced plants was smaller than that of control plants.Physiological analyses showed that the activity of superoxide dismutase(SOD) and peroxidase(POD) and the content of proline(Pro) in SL-ZH13-silenced plants were lower than those in control plants after 1.5 and 3 h of drought stress treatment.The malondialdehyde(MDA) content in SL-ZH13-silenced plants was higher than that in control plants after 1.5 and 3 h of drought stress treatment,and H2O2 and O2^-· accumulated much more in the leaves of SL-ZH13-silenced plants than in the leaves of control plants.These results suggested that silencing the SL-ZH13 gene affected the response of tomato plants to drought stress and decreased the drought tolerance of tomato plants.
基金This work was supported by the National Natural Science Foundation of China （No. 30972526） and by the Applied Basic Research Programs of Sichuan Province （No. 20141Y0110）. The authors thank Prof. Stanley Lin for his assistance in revising the final draft of the manuscript and editing for English grammar and syntax.
文摘To investigate whether transcription of hepatitis B virus （HBV） gene occurs in human sperm, total RNA was extracted from sperm of patients with chronic HBV infection （test-I）, from donor sperm transfected with a plasmid containing the full-length HBV genome （test-2）, and from nontransfected donor sperm （control）, used as the template for reverse transcription-polymerase chain reaction （RT-PCR）. Positive bands for HBV DNA were observed in the test groups but not in the control. Next, to identify the role of host genes in regulating viral gene transcription in sperm, total RNA was extracted from 2-cell embryos derived from hamster oocytes fertilized in vitro by HBV-transfected （test） or nontransfected （control） human sperm and successively subjected to SMART-PCR, suppression subtractive hybridization, T/A cloning, bacterial amplification, microarray hybridization, sequencing and the Basic Local Alignment Search Tool （BLAST） search to isolate differentially expressed genes. Twenty-nine sequences showing significant identity to five human gene families were identified, with chorionic somatomammotropin hormone 2 （CSH2）, eukaryotic translation initiation factor 4 gamma 2 （EIF4G2）, pterin-4 alpha-carbinolamine dehydratase 2 （PCBD2）, pregnancy-specific beta-l-glycoprotein 4 （PSG4） and titin （TTN） selected to represent target genes. Using real-time quantitative RT-PCR （qRT-PCR）, when CSH2 and PCBD2 （or EIF4G2, PSG4 and TTN） were silenced by RNA interference, transcriptional levels of HBV s and x genes significantly decreased （or increased） （P 〈 0.05）. Silencing of a control gene in sperm did not significantly change transcription of HBV s and x genes （P 〉 0.05）. This study provides the first experimental evidence that transcription of HBV genes occurs in human sperm and is regulated by host genes.
基金funded by the National Natural Science Foundation of China (30771387)the Commonweal Research Program of Agricultural Science of China (nyhyzx3-16)+2 种基金the Research Foundation of Education Bureau of Hunan Province, China (06B027)the Natural Science Foundation of Hunan Province in China (10JJ2030)the Scientific Research Starting Foundation for Doctors of Hunan University of Science and Technology, China (E50563)
文摘WRKY transcription factors are involved in the regulation of response to biotic and abiotic stresses in plants. A full-length cDNA clone of rice WRKY82 gene （OsWRKY82） was isolated from a cDNA library generated from leaves infected by Magnaporthe grisea. OsWRKY82 contained an entire open reading frame in length of 1 701 bp, and was predicted to encode a polypeptide of 566 amino acid residues consisting of two WRKY domains, each with a zinc finger motif of C2H2, belonging to the WRKY subgroup I. OsWRKY82 shared high identity at the amino acid level with those from Sorghum bicolor, Hordeum vulgare, and Zea mays. The transcript level of OsWRKY82 was relatively higher in stems, leaves, and flowers, and less abundant in grains. It was induced by inoculation with M. grisea and Rhizoctonia solani. However, the inducible expression in incompatible rice-M. grisea interactions was earlier and greater than that in compatible interactions. The expression of OsWRKY82 was up-regulated by methyl jasmonate and ethephon, whereas salicylic acid exerted no effects on its expression. Moreover, OsWRKY82 exhibited transcriptional activation ability in yeast. Additionally, OsWRKY82 transcripts could be induced by wounding and heat shocking, but not by abscisic acid, cold, high salinity and dehydration. By contrast, gibberellin suppressed the expression of OsWRKY82. These indicate that OsWRKY82 is a multiply stress-inducible gene responding to both biotic and abiotic stresses, and may be involved in the regulation of defense response to pathogens and tolerance against abiotic stresses by jasmonic acid/ethylene-dependent signaling pathway.
文摘The human RNA methyltransferase like i gene(RNMTL1)is one of thirteen newly discovered geneswithin a 116 Kb segment of the chromosome 17p13.3 that suffers from a high frequent loss of heterozygosityin human hepatocellular carcinoma in China[1-5].To understand the molecular mechanisms underlyingtranscription control of the RNMTL1 gene in human cancers,we decline using of the conventional approachwhere the cis-elements bound by the known transcription factors are primary targets,and carried out thesystematic analyses to dissect the promoter structure and identify/characterize the key cis-elements thatare responsible for its strong expression in cell.The molecular approaches applied included 1,the primerextension for mapping of the transcription starts;2,the transient transfection/reporter assays on a largenumber of deletion and site-specific mutants of the promoter segment for defining the minimal promoterand the crucial elements within;and 3,the electrophoresis mobility shift assay with specific antibodies forreconfirming the nature of the transcription factors and their cognate cis-elements.We have shown that theinteraction of an ATF/CREB element(-38 to-31)and its cognate transcription factors play a predominantrole in the promoter activity of the RNMTL1 gene.The secondary DNA structures of the ATF/CREBelement play a more vital role in the protein-DNA interaction.Finally,we reported a novel mechanismunderlying the YY1 mediated transcription repression,namely,the ATF/CREB dependent transcription-repression by YY1 is executed in absence of its own sequence-specific binding.
基金supported by the National Natural Science Foundation of China (Grant No. 32071816)the Opening Preject of State Key Laboratory of Tree Genetics and Breeding (Grant No. K2021101)Special Fund for Beijing Common Construction Project。
文摘Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription factors play important regulatory roles in growth, development,dormancy and abiotic stress. To date, bZIP transcription factors have not been systematically studied in P. mume. In this study, 49 bZIP genes were first identified in P. mume, and the PmbZIP family was divided into 12 groups according to the grouping principles for the Arabidopsis thaliana bZIP family. For the first time, we constructed a detailed model of the PmbZIP domains(R-x_(3)–N-(x)_7-R/K-x_(2)-K-x_(6)-L-x_(6)-L-_(6)-L). Phylogenetic and synteny analyses showed that PmbZIPs duplication events might have occurred during the large-scale genome duplication events. A relatively short time of speciation and the finding that 91.84% of the bZIP genes formed orthologous pairs between P. mume and Prunus armeniaca provided evidence of a close relationship. Gene expression patterns were analysed in different tissues and periods, indicating that PmbZIP genes with the same motifs exhibited similar expression patterns. The gene expression results showed that PmbZIP31/36/41 genes played a more prominent role in the response to freezing stress than cold stress. The expression level of almost all subset Ⅲ genes was upregulated under freezing treatment, especially after cold exposure. We analysed the gene expression patterns of PmbZIP12/31/36/41/48 and their responses to low-temperature stress, which provided useful resources for future studies on the cold/freezing-tolerant molecular breeding of P. mume.
基金Project supported by the Key Project of Hebei North University(No.120177)the Science and Technology Bureau Research Development Plan of Zhangjiakou City in Hebei(No.0911021D-4)China
文摘Axon regeneration is crucial for recovery from neurological diseases. Numerous studies have identified several genes, microRNAs （miRNAs）, and transcription factors （TFs） that influence axon regeneration. However, the regulatory networks involved have not been fully elucidated. In the present study, we analyzed a regulatory network of 51 miRNAs, 27 TFs, and 59 target genes, which is involved in axon regeneration. We identified 359 pairs of feed- forward loops （FFLs）, seven important genes （Naplll, Arhgef12, Sema6d, Akt3, Trim2, Rabllfip2, and Rps6ka3）, six important miRNAs （hsa-miR-204-5p, hsa-miR-124-3p, hsa-miR-26a-5p, hsa-miR-16-5p, hsa-miR-17-5p, and hsa- miR-15b-5p）, and eight important TFs （Smada2, Flil, Wtl, Sp6, Sp3, Smad4, Smad5, and Crebl）, which appear to play an important role in axon regeneration. Functional enrichment analysis revealed that axon-associated genes are involved mainly in the regulation of cellular component organization, axonogenesis, and cell morphogenesis during neuronal differentiation. However, these findings need to be validated by further studies.
基金Supported by the Agriculture Science&Technology Achievements Transformation Fund(No.2011GB24910005)the Modern Agricultural-Industry Technology Research Project(No.200903030)+2 种基金the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A406)the Shandong Agriculture Breeding Engineering Biological Resources Innovation of Research Projectthe National"Twelfth Five-Year"Plan for Science&Technology Support(No.2013BAB01B01)
文摘Saccharina japonica is a common macroalga in sublittoral communities of cold seawater environments, and consequently may have highly efficient ribulose-1, 5-bisphosphate carboxylase/ oxygenase （Rubisco） activity for carbon assimilation. In our study, we cloned the full-length Rubisco gene from S.japonica （SJ-rbc）. It contained an open reading frame for a large subunit gene （SJ-rbcL） of 1 467 bp, a small subunit gene （SJ-rbcS） of 420 bp, and a SJ-rbcL/S intergenie spacer of 269 bp. The deduced peptides of SJ-rbcL and SJ-rbcS were 488 and 139 amino acids with theoretical molecular weights and isoelectric points of 53.97 kDa, 5.81 and 15,84 kDa, 4.71, respectively. After induction with 1 mmol/L isopropyl-β-D- thiogalactopyranoside for 5 h and purification by Ni2＋ affinity chromatography, electrophoresis and western blot detection demonstrated successful expression of the 55 kDa SJ-rbcL protein. Real-time quantitative PCR showed that the mRNA levels of SJ-rbcL in gametophytes increased when transferred into normal growth conditions and exhibited diurnal variations： increased expression during the day but suppressed expression at night. This observation implied that Rubisco played a role in normal gametophytic growth and development. In juvenile sporophytes, mRNA levels of SJ-rbcL, carbonic anhydrase, Calvin-Benson- Bassham cycle-related enzyme, and chloroplast light-harvesting protein were remarkably increased under continuous light irradiance. Similarly, expression of these genes was up-regulated under blue light irradiance at 350 umol/（m2.s）. Our results indicate that long-term white light and short-term blue light irradiance enhances juvenile sporophytic growth by synergistic effects of various photosynthetic elements.
基金supported by the Natural Science Foundation of Hebei(Grant No.C2021209005)National Natural Science Foundation of China(Grant No.32172583)+1 种基金the Natural Science Foundation for Distinguished Young Scholar of Hebei Province(Grant No.C2022209010)the China Postdoctoral Science Foundation(Grant Nos.2020M673188,2021T140097).
文摘Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.
基金Project supported by the National Natural Science Foundation of China (Grant No.10865006)the Science Foundation of Yunnan University (Grant No.2009A01Z)
文摘This paper investigates the stochastic resonance （SR） induced by a multiplicative periodic signal in the gene transcriptional regulatory system with correlated noises. The expression of the signal-to-noise ratio （SNR） is derived. The results indicate that the existence of a maximum in SNR vs. the additive noise intensity α the multiplicative noise intensity D and the cross-correlated noise intensity λ is the identifying characteristic of the SR phenomenon and there is a critical phenomenon in the SNR as a function of λ, i.e., for the case of smaller values of noise intensity （α or D）, the SNR decreases as λ increases; however, for the case of larger values of noise intensity （α or D）, the SNR increases as λ increases.
