Transcriptional Regulatory Factors Research Articles

Identification of Grape Laccase Genes and Their Potential Role in Secondary Metabolite Synthesis.

Laccase, a copper-containing oxidoreductase, has close links with secondary metabolite biosynthesis in plants. Its activity can affect the synthesis and accumulation of secondary metabolites, thereby influencing plant growth, development, and stress resistance. This study aims to identify the grape laccases (VviLAC) gene family members in grape (Vitis vinifera L.) and explore the transcriptional regulatory network in berry development. Here, 115 VviLACs were identified and divided into seven (Type I-VII) classes. These were distributed on 17 chromosomes and out of 47 VviLACs on chromosome 18, 34 (72.34%) were involved in tandem duplication events. VviLAC1, VviLAC2, VviLAC3, and VviLAC62 were highly expressed before fruit color development, while VviLAC4, VviLAC12, VviLAC16, VviLAC18, VviLAC20, VviLAC53, VviLAC60 and VviLAC105 were highly expressed after fruit color transformation. Notably, VviLAC105 showed a significant positive correlation with important metabolites including resveratrol, resveratrol dimer, and peonidin-3-glucoside. Analysis of the transcriptional regulatory network predicted that the 12 different transcription factors target VviLACs genes. Specifically, WRKY and ERF were identified as potential transcriptional regulatory factors for VviLAC105, while Dof and MYB were identified as potential transcriptional regulatory factors for VviLAC51. This study identifies and provides basic information on the grape LAC gene family members and, in combination with transcriptome and metabolome data, predicts the upstream transcriptional regulatory network of VviLACs.

Integrating protein interaction and pathway crosstalk network reveals a promising therapeutic approach for psoriasis through apoptosis induction

Psoriasis is a complex inflammatory skin disease manifested by altered proliferation and differentiation of keratinocytes with dysfunctional apoptosis. This study aimed to identify regulatory factors and comprehend the underlying mechanisms of inefficient apoptosis to open up promising therapeutic approaches. Incorporating human protein interactions, apoptosis proteins, and physical relationships of psoriasis-apoptosis proteins helped us to generate a psoriasis-apoptosis interaction (SAI) network. Subsequently, topological and functional analyses of the SAI network revealed effective proteins, functional modules, hub motifs, dysregulated pathways and transcriptional gene regulatory factors. Network pharmacology, molecular docking and molecular dynamics simulation methods identified the potential drug-target interactions. RELA, MAPK1, MAPK3, MMP9, IL1B, AKT1 and STAT1 were revealed as effective proteins. The MAPK1-MAPK3-RELA motif was identified as a hub regulator in the crosstalk between 41 pathways. Among all pathways, “lipid and atherosclerosis” was found to be the predominant pathway. Acetylcysteine, arsenic-trioxide, β-elemene, bortezomib and curcumin were identified as potential drugs to inhibit pathway crosstalk. Experimental verifications were performed using the literature search, GSE13355 and GSE14905 microarray datasets. Drug-protein-pathway interactions associated with apoptosis were deciphered. These findings highlight the role of hub motif-mediated pathway-pathway crosstalk associated with apoptosis in the complexity of psoriasis and suggest crosstalk inhibition as an effective therapeutic approach.

Comparative analysis of the transcriptomes from regenerated plants and root explants of endangered Oplopanax elatus.

Oplopanax elatus is a plant of therapeutic significance in oriental medicine; however, its mass cultivation is limited owing to the difficulties in propagating it from seeds. In this study, we investigated the transcriptome profiles and transcriptional regulatory factors expressed during plantlet regeneration from root tissues of the endangered O. elatus. The RNA-seq results for the control and regenerated plants cultured in liquid medium for 8weeks showed that the clean length of the control group was 11,901,667,912 and that of the 8-week sample was 10,115,155,171, indicating a clean value of 97% for both samples. The number of mapped paired-end reads was 63,922,480 for the control group and 54,146,902 for the 8-week sample. The number of genes for which at least one clean data point was mapped was 43,177 in the control group and 42,970 in the 8-week sample. The results of the differentially expressed gene analysis indicate that the number of upregulated genes in the 8-week sample was 158, and the number of downregulated genes was 424. Gene Ontology (GO) analysis of the upregulated genes revealed that GO terms were classified into 14 categories, and genes expressed in the biological process category occurred most frequently. GO terms of the downregulated genes were evenly distributed into two categories: biological process and molecular function. From the upregulated genes, eight reference genes with significant differences in expression were selected and analyzed using real-time PCR. The Oe38836 gene (late embryogenesis abundant protein M17-like isoform X1) showed the highest expression rate that was more than tenfold that of the control. Oe40610 (auxin-responsive protein SAUR21-like) and Oe07114 (glucose-1-phosphate adenyl transferase-like protein) genes showed expression levels that were increased eightfold relative to the control. The RNA sequencing (RNA-seq) results from the plants regenerated through liquid culture of O. elatus root tissue were confirmed using real-time PCR, indicating their reliability.

Understanding Bacillus response to salt stress: Growth inhibition, enhanced EPS secretion, and molecular adaptation mechanisms

This study investigates the secretion pattern of extracellular polymeric substances (EPS) by Bacillus sp. under varying salt concentrations and elucidates the molecular mechanisms governing EPS synthesis and secretion. Salt stress inhibited cell proliferation, while optimal salt stimulation promoted EPS secretion, resulting in increased viscosity of the culture medium and the formation of bacterial clusters. Fourier infrared spectrum analysis revealed functional groups such as C-O-C and N-H within the EPS. Soluble-EPS (S-EPS) contained sulfur and phosphorus groups associated with heavy metal ions adsorption. The study also identified a novel polysaccharide formed through bonding EPS (B-EPS). High salt concentrations correlated with elevated levels of tryptophan protein and its derivatives, increased tyrosine polysaccharide derivatives, and decreased aromatic polysaccharides. B-EPS exhibited higher levels of aromatic polysaccharides, with Na+ promoting detachment of B-EPS from the cell surface. Transcriptome sequencing (RNA-seq) analysis under salt stress revealed significant expression of spore kinase (KinD) and response regulatory protein Spo0A in the phosphoric acid relay system. Key transcriptional regulatory factors, including OmpR and exopolysaccharide biosynthesis, were closely associated with EPS synthesis and secretion. This study establishes a theoretical foundation for the industrial production and practical application of EPS by elucidating the molecular mechanisms underlying Bacillus' response to salt stress.

Dicranopteris dichotoma rhizosphere-derived Bacillus sp. MQB12 acts as an enhancer of plant growth via increasing phosphorus utilization, hormone synthesis, and rhizosphere microbial abundance

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents.Graphical

Compensatory evolution of chromosomes and plasmids counteracts the plasmid fitness cost.

Plasmids incur a fitness cost that has the potential to restrict the dissemination of resistance in bacterial pathogens. However, bacteria can overcome this disadvantage by compensatory evolution to maintain their resistance. Compensatory evolution can occur via both chromosomes and plasmids, but there are a few reviews regarding this topic, and most of them focus on plasmids. In this review, we provide a comprehensive overview of the currently reported mechanisms underlying compensatory evolution on chromosomes and plasmids, elucidate key targets regulating plasmid fitness cost, and discuss future challenges in this field. We found that compensatory evolution on chromosomes primarily arises from mutations in transcriptional regulatory factors, whereas compensatory evolution of plasmids predominantly involves three pathways: plasmid copy number regulation, conjugation transfer efficiency, and expression of antimicrobial resistance (AMR) genes. Furthermore, the importance of reasonable selection of research subjects and effective integration of diverse advanced research methods is also emphasized in our future study on compensatory mechanisms. Overall, this review establishes a theoretical framework that aims to provide innovative ideas for minimizing the emergence and spread of AMR genes.

Multilevel regulation of lactose operon in Bacillus licheniformis: Coordination of LacR, CcpA and TnrA regulators

Previous research has confirmed the involvement of the lac1 gene cluster in lactose metabolism in Bacillus licheniformis, which is able to co-utilize lactose and low concentrations of glucose or certain carbon sources. However, the internal regulatory mechanisms underlying specific lactose utilization remain elusive. In this study, we conducted a comprehensive investigation to elucidate the modulation mechanism of the lac1 gene cluster. We discovered a 162 bp bidirectional promoter located between the lacDCAB and lacR genes, which encodes a GntR family transcriptional regulatory factor. A 38 bp perfectly palindromic sequence (BOX1) within this promoter is critical for inducing lac1 expression. LacR and CcpA were shown to bind specifically to BOX1, and their novel binding motifs were identified. In BL2ΔlacR, BL2ΔccpA, and BL2ΔlacRΔccpA mutant strains, we confirmed the differential inhibitory levels of LacR and CcpA on bidirectional promoters. Furthermore, it was demonstrated that TnrA also binds BOX1 and exerts a positive regulatory effect on the lac1 cluster. Finally, we proposed a novel model to unravel the complex molecular interactions controlling the expression of the lac1 gene. These insights provide a foundation for exploring rational design strategies to optimize lactose fermentation processes and improve the efficiency of industrial lactose utilization.

ID2-ETS2 axis regulates the transcriptional acquisition of pro-tumoral microglia phenotype in glioma

Glioblastoma is a highly aggressive brain tumour that creates an immunosuppressive microenvironment. Microglia, the brain’s resident immune cells, play a crucial role in this environment. Glioblastoma cells can reprogramme microglia to create a supportive niche that promotes tumour growth. However, the mechanisms controlling the acquisition of a transcriptome associated with a tumour-supportive microglial reactive state are not fully understood. In this study, we investigated changes in the transcriptional profile of BV2 microglia exposed to C6 glioma cells. RNA-sequencing analysis revealed a significant upregulation of microglial inhibitor of DNA binding 1 (Id1) and Id2, helix-loop-helix negative transcription regulatory factors. The concomitant regulation of microglial ETS proto-oncogene 2, transcription factor (ETS2)-target genes, i.e., Dusp6, Fli1, Jun, Hmox1, and Stab1, led us to hypothesize that ETS2 could be regulated by ID proteins. In fact, ID2-ETS2 protein interactions increased in microglia exposed to glioma cells. In addition, perturbation of the ID2-ETS2 transcriptional axis influenced the acquisition of a microglial tumour-supportive phenotype. ID2 and ETS2 genes were found to be expressed by the tumour-associated microglia isolated from human glioblastoma tumour biopsies. Furthermore, ID2 and ETS2 gene expressions exhibited inverse prognostic values in patients with glioma in cohorts from The Cancer Genome Atlas. Collectively, our findings indicate that the regulation of ETS2 by ID2 plays a role in the transcriptional regulation of microglia in response to stimuli originating from glioblastoma cells, information that could lead to developing therapeutic strategies to manipulate microglial tumour-trophic functions.

Assessment of ID family proteins expression in colorectal cancer of Iraqi patients.

Colorectal cancer (CRC) is the second most deathly worldwide and third most common cancer, CRC is a very heterogeneous disease where tumors can form by both environmental and genetic risk factors and includes epigenetic and genetic alternations. Inhibitors of DNA binding proteins (ID) are a class of helix-loop-helix transcription regulatory factors; these proteins are considered a family of four highly preserved transcriptional regulators (ID1-4), shown to play significant roles in many processes that are associated with tumor development. ID family plays as negatively dominant antagonists of other essential HLH proteins, concluding the creation of non-functional heterodimers and regulation of the transcription process. 120 Fresh tissue and blood samples Forty (40) samples of fresh tissue and blood were collected from patients diagnosed with CRC, twenty (20) samples were collected from a patient diagnosed as healthy. The (qRT-PCR) method is a sensitive technique for the quantifying of steady-state mRNA levels that used to evaluation the expression levels of ID (1-4) gene. The findings indicate downregulation in ID1 in tissue with a highly significant change between patients and control groups, where upregulation in the ID1 gene is shown in blood samples.ID2 gene also demonstrated high significant change where show upregulation in tissue and downregulation in blood sample. ID3 and ID4 genes show downregulation in tissue and blood samples with a significant change in ID3 blood samples between patient and blood groups. Because of the regulation function of the ID family in many processes, the up or down regulation of IDs genes in tumors Proves how important its tumor development, and therefore those proteins can be used as an indicator for CRC.

Comparative Analysis of Physiological Responses and Intestinal Microbiota in Juvenile Soft-Shelled Turtle (Pelodiscus sinensis) Fed Four Types of Dietary Carbohydrates.

A 60 day feeding trial was conducted to evaluate the impacts of dietary carbohydrates with different complexities and configurations on the growth, plasma parameters, apparent digestibility, intestinal microbiota, glucose, and lipid metabolism of soft-shelled turtles (Pelodiscus sinensis). Four experimental diets were formulated by adding 170 g/kg glucose, fructose, α-starch, or cellulose, respectively. A total of 280 turtles (initial body weight 5.11 ± 0.21 g) were distributed into 28 tanks and were fed twice daily. The results showed that the best growth performance and apparent digestibility was observed in the α-starch group, followed by the glucose, fructose, and cellulose groups (p < 0.05). Monosaccharides (glucose and fructose) significantly enhanced the postprandial plasma glucose levels and hepatosomatic index compared to polysaccharides, due to the un-inhibited gluconeogenesis (p < 0.05). Starch significantly up-regulated the expression of the genes involved in glycolysis, pentose phosphate pathway, lipid anabolism and catabolism, and the transcriptional regulation factors of glycolipid metabolism (srebp and chrebp) (p < 0.05), resulting in higher plasma triglyceride levels and lipid contents in the liver and the whole body. The fructose group exhibited a lower lipid deposition compared with the glucose group, mainly by inhibiting the expression of srebp and chrebp. Cellulose enhanced the proportion of opportunistic pathogenic bacteria. In conclusion, P. sinensis utilized α-starch better than glucose, fructose, and cellulose.

Elevated expression of ELK1 promotes breast cancer cell growth and correlates with poor prognosis of breast cancer patients

Background: Breast cancer is the most common tumor in women and poses a serious threat to women’s physical and mental health. The ETS-like gene 1 (ELK1), upregulated in various malignancies, serves as a transcription regulatory factor. This study primarily investigates the biological functions and prognostic significance of ELK1 in breast cancer. Materials and Methods: We conducted an analysis of ELK1 expression in breast cancer and adjacent tissues using data from The Cancer Genome Atlas (TCGA), and validated these findings with clinical specimens. Additionally, we employed siRNA transfection, proliferation and apoptosis assays to elucidate the roles of ELK1 in breast cancer cells. Furthermore, we assessed the correlations between ELK1 expression and the tumor microenvironment, as well as tumor-infiltrating immune cells (TIICs), utilizing the ESTIMATE and CIBERSORT algorithms. Finally, we used Kaplan-Meier plots and COX regressions to identify prognostic factors, and developed a predictive alignment diagram to evaluate the prognostic significance of ELK1 in breast cancer. Results: A marked increase in ELK1 expression is evident in breast cancer tissues (P&lt;0.01). Experimental findings demonstrate that silencing ELK1 suppresses proliferation and promotes apoptosis in breast cancer cells. ELK1 plays a pivotal role in regulating the immune microenvironment of breast cancer. Furthermore, the alignment diagram indicates that ELK1 may serve as an independent prognostic factor for breast cancer patients. Conclusion: Our study reveals that ELK1 exhibits high expression level in breast cancer tissues and is associated with disease progression and poor prognosis.

An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.

In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria. This includes the components of the dedicated mitochondrial transcription and replication systems and regulatory factors, which are entirely distinct from the information processing systems in the nucleus. However, since the 1990s several nuclear transcription factors have been reported to act in mitochondria, and previously we identified 8 human and 3 mouse transcription factors (TFs) with strong localized enrichment over the mitochondrial genome using ChIP-seq (Chromatin Immunoprecipitation) datasets from the second phase of the ENCODE (Encyclopedia of DNA Elements) Project Consortium. Here, we analyze the greatly expanded in the intervening decade ENCODE compendium of TF ChIP-seq datasets (a total of 6,153 ChIP experiments for 942 proteins, of which 763 are sequence-specific TFs) combined with interpretative deep learning models of TF occupancy to create a comprehensive compendium of nuclear TFs that show evidence of association with the mitochondrial genome. We find some evidence for chrM occupancy for 50 nuclear TFs and two other proteins, with bZIP TFs emerging as most likely to be playing a role in mitochondria. However, we also observe that in cases where the same TF has been assayed with multiple antibodies and ChIP protocols, evidence for its chrM occupancy is not always reproducible. In the light of these findings, we discuss the evidential criteria for establishing chrM occupancy and reevaluate the overall compendium of putative mitochondrial-acting nuclear TFs.

Fish oil replacement with different vegetable oils in Onychostoma macrolepis: Effects on fatty acid metabolism based on whole-body fatty acid balance method and genes expression.

To evaluate the fatty acid (FA) metabolism status and possibility as a DHA source of farmed Onychostoma macrolepis, a total of 168 fish (2.03 ± 0.23 g) were fed four diets supplemented with fish oil (FO), linseed oil (LO), soybean oil (SO), and a mixture of LO and SO oil (MO), respectively, for 70 days. Body FA compositions were modified reflecting dietary FAs. Comparing liver and intestine fatty acids with fish fed four diets, the content of ARA in fish fed SO was significantly higher than others (P < 0.05), but showed no difference in muscle. The tissue FA profile showed that the FO-fed group successfully deposited DHA, while the LO-fed group converted ALA to DHA effectively, as well as the liver and intestine EPA was notably highest in the FO group, whereas no difference between the FO and LO group in the muscle. The FA results showed that the DHA contents in the muscle of Onychostoma macrolepis are at a medium-high level compared with several other fish species with the highest aquaculture yield. Correspondingly, in the fish fed diet with LO, SO, and MO, the genes of most FA biosynthesis, transportation, and transcriptional regulation factors were increased in the liver and muscle, but no significant difference was observed in the gene expression of Elovl4b, FATP1, and FABP10 in the muscle. In addition, the enzyme activity involved in PUFA metabolism was higher in fish fed vegetable oil-based diets, corroborating the results of the gene expression. Increased in vivo elongase and desaturase (Δ5, Δ6, and Δ9) activities were recorded in fish fed fish oil-devoid diets, which resulted in the appearance of products associated with elongase and desaturase activities in fish. Besides, as the specific n-3 PUFA synthesis substrate, the dietary supplementation of ALA not only retains most of the nutrition value but also ensures the muscular texture, such as fiber diameter and density. It is concluded that farmed O. macrolepis owns strong n-3 LC-PUFA biosynthetic capacity and high DHA contents so it can be a good DHA source for the population.

Human T-cell lymphotropic virus type 1 (HTLV-1) grip on T-cells: investigating the viral tapestry of activation

IntroductionHuman T-cell Lymphotropic virus type 1 (HTLV-1) belongs to retroviridae which is connected to two major diseases, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and Adult T-cell leukemia/lymphoma (ATLL). This study aims to investigate the mRNA expressions of key proteins correlated to T-cell activation in asymptomatic carriers (ACs) HTLV-1 infected patients, shedding light on early molecular events and T-cell activation following HTLV-1 infection.Material and MethodsThe study involved 40 participants, including 20 ACs and 20 healthy subjects. Blood samples were collected, ELISA assessment for screening and confirmation with PCR for Trans-activating transcriptional regulatory protein (Tax) and HTLV-1 basic leucine zipper factor (HBZ) of the HTLV-1 were done. mRNA expressions of C-terminal Src kinase (CSK), Glycogen Synthase Kinase-3 Beta (GSK3β), Mitogen-Activated Protein Kinase 14 (MAP3K14 or NIK), Phospholipase C Gamma-1 (PLCG1), Protein Tyrosine Phosphatase non-Receptor Type 6 (PTPN6) and Mitogen-Activated Protein Kinase Kinase Kinase-7 (SLP-76) and Mitogen-Activated Protein Kinase14 (MAP3K7 or TAK1) were assayed using RT-qPCR. Statistical analyses were performed using PRISM and SPSS software.ResultsWhile there were no significant upregulation in CSK and PTPN6 in ACs compared to healthy individuals, expression levels of GSK3β, MAP3K14, PLCG1, SLP-76, and TAK1 were significantly higher in ACs compared to healthy subjects which directly contributes to T-cell activation in the HTLV-1 ACs.ConclusionHTLV-1 infection induces differential mRNA expressions in key proteins associated with T-cell activation. mRNAs related to T-cell activation showed significant upregulation compared to PTPN6 and CSK which contributed to T-cell regulation. Understanding these early molecular events in ACs may provide potential markers for disease progression and identify therapeutic targets for controlling viral replication and mitigating associated diseases. The study contributes novel insights to the limited literature on T-cell activation and HTLV-1 pathogenesis.

Tannic acid inhibits Escherichia coli biofilm formation and underlying molecular mechanisms: Biofilm regulator CsgD

Biofilms often engender persistent infections, heightened antibiotic resistance, and the recurrence of infections. Therefor, infections related to bacterial biofilms are often chronic and pose challenges in terms of treatment. The main transcription regulatory factor, CsgD, activates csgABC-encoded curli to participate in the composition of extracellular matrix, which is an important skeleton for biofilm development in enterobacteriaceae. In our previous study, a wide range of natural bioactive compounds that exhibit strong affinity to CsgD were screened and identified via molecular docking. Tannic acid (TA) was subsequently chosen, based on its potent biofilm inhibition effect as observed in crystal violet staining. Therefore, the aim of this study was to investigate the specific effects of TA on the biofilm formation of clinically isolated Escherichia coli (E. coli). Results demonstrated a significant inhibition of E. coli Ec032 biofilm formation by TA, while not substantially affecting the biofilm of the ΔcsgD strain. Moreover, deletion of the csgD gene led to a reduction in Ec032 biofilm formation, alongside diminished bacterial motility and curli synthesis inhibition. Transcriptomic analysis and RT-qPCR revealed that TA repressed genes associated with the csg operon and other biofilm-related genes. In conclusion, our results suggest that CsgD is one of the key targets for TA to inhibit E. coli biofilm formation. This work preliminarily elucidates the molecular mechanisms of TA inhibiting E. coli biofilm formation, which could provide a lead structure for the development of future antibiofilm drugs.

Engineering Fatty Acid Biosynthesis in Microalgae: Recent Progress and Perspectives.

Microalgal lipids hold significant potential for the production of biodiesel and dietary supplements. To enhance their cost-effectiveness and commercial competitiveness, it is imperative to improve microalgal lipid productivity. Metabolic engineering that targets the key enzymes of the fatty acid synthesis pathway, along with transcription factor engineering, are effective strategies for improving lipid productivity in microalgae. This review provides a summary of the advancements made in the past 5 years in engineering the fatty acid biosynthetic pathway in eukaryotic microalgae. Furthermore, this review offers insights into transcriptional regulatory mechanisms and transcription factor engineering aimed at enhancing lipid production in eukaryotic microalgae. Finally, the review discusses the challenges and future perspectives associated with utilizing microalgae for the efficient production of lipids.

Inhibitory potential of Syzygium aromaticum against Fusarium oxysporum f. sp. lycopersici: In-vitro analysis and molecular docking studies

The antifungal potential of the extract of cloves (Syzygium aromaticum) was investigated in this study. The crude extracts of cloves and n-hexane, chloroform and n-butanol fractions were prepared. The antifungal activity of obtained fractions was studied at various concentrations ranging from 1.5 to 200.00 µg/mL. Thiophanate methyl (TM) was used as +ve control in this study. The fractions including methanolic, n-hexane, n-butanol, and chloroform significantly inhibited the growth of Fusarium oxysporum f.sp. lycopersici (FOL) ranging from 93.8 to 100 % when used at 200 µg/mL. The chloroform fraction showed 6.25 µg/mL MIC as compared to TM with 64 µg/mL MIC. GC/MS analysis showed that the chloroform fraction contained Eugenol, Phenol, 2,2′-methylenebis[6-(1,1-dimethylethyl)-4-methyl, 2,4-Di‑tert-butylphenol, n-Hexadecanoic acid, Phenol, and 2‑methoxy-4-(2-propenyl)- acetate. The findings of in-vitro antifungal analysis were further supported by molecular docking studies. Two virulence proteins of FOL i.e., global transcription regulator (SGE1) and DNA binding transcription factor (STE12) were docked with identified phytocompounds in the chloroform fraction by GC/MS analysis. Both of the receptors showed maximum binding affinities with 2-[2-(4-Phenyl-piperidin-1-yl)-ethyl]-isoindole-1,3‑dione (PED) (-12.054 kcal/mol) and 3,5-di‑tert-Butyl-4-hydroxyphenylpropionic acid (BHP) (-13.327 kcal/mol) respectively with strong hydrophilic/phobic interactions with active pocket residues. In conclusion, the chloroform fraction of S. aromaticum can be used to manage FOL.

Improving the production of carbamoyltobramycin by an industrial Streptoalloteichus tenebrarius through metabolic engineering

Tobramycin is an essential and extensively used broad-spectrum aminoglycoside antibiotic obtained through alkaline hydrolysis of carbamoyltobramycin, one of the fermentation products of Streptoalloteichus tenebrarius. To simplify the composition of fermentation products from industrial strain, the main byproduct apramycin was blocked by gene disruption and constructed a mutant mainly producing carbamoyltobramycin. The generation of antibiotics is significantly affected by the secondary metabolism of actinomycetes which could be controlled by modifying the pathway-specific regulatory proteins within the cluster. Within the tobramycin biosynthesis cluster, a transcriptional regulatory factor TobR belonging to the Lrp/AsnC family was identified. Based on the sequence and structural characteristics, tobR might encode a pathway-specific transcriptional regulatory factor during biosynthesis. Knockout and overexpression strains of tobR were constructed to investigate its role in carbamoyltobramycin production. Results showed that knockout of TobR increased carbamoyltobramycin biosynthesis by 22.35%, whereas its overexpression decreased carbamoyltobramycin production by 10.23%. In vitro electrophoretic mobility shift assay (EMSA) experiments confirmed that TobR interacts with DNA at the adjacent tobO promoter position. Strains overexpressing tobO with ermEp* promoter exhibited 36.36% increase, and tobO with kasOp* promoter exhibited 22.84% increase in carbamoyltobramycin titer. When the overexpressing of tobO and the knockout of tobR were combined, the production of carbamoyltobramycin was further enhanced. In the shake-flask fermentation, the titer reached 3.76 g/L, which was 42.42% higher than that of starting strain. Understanding the role of Lrp/AsnC family transcription regulators would be useful for other antibiotic biosynthesis in other actinomycetes.Key points• The transcriptional regulator TobR belonging to the Lrp/AsnC family was identified. • An oxygenase TobO was identified within the tobramycin biosynthesis cluster.• TobO and TobR have significant effects on the synthesis of carbamoyltobramycin.

SIRT1 and ZNF350 as novel biomarkers for osteoporosis: a bioinformatics analysis and experimental validation.

Osteoporosis (OP) is characterized by bone mass decrease and bone tissue microarchitectural deterioration in bone tissue. This study identified potential biomarkers for early diagnosis of OP and elucidated the mechanism of OP. Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) for the GSE56814 dataset. A gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) to identify key modules associated with healthy and OP samples. Functional enrichment analysis was conducted using the R clusterProfiler package for modules to construct the transcriptional regulatory factor networks. We used the "ggpubr" package in R to screen for differentially expressed genes between the two samples. Gene set variation analysis (GSVA) was employed to further validate hub gene expression levels between normal and OP samples using RT-PCR and immunofluorescence to evaluate the potential biological changes in various samples. There was a distinction between the normal and OP conditions based on the preserved significant module. A total of 100 genes with the highest MM scores were considered key genes. Functional enrichment analysis suggested that the top 10 biological processes, cellular component and molecular functions were enriched. The Toll-like receptor signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, osteoclast differentiation, JAK-STAT signaling pathway, and chemokine signaling pathway were identified by Kyoto Encyclopedia of Genes and Genomes pathway analysis. SIRT1 and ZNF350 were identified by Wilcoxon algorithm as hub differentially expressed transcriptional regulatory factors that promote OP progression by affecting oxidative phosphorylation, apoptosis, PI3K-Akt-mTOR signaling, and p53 pathway. According to RT-PCR and immunostaining results, SIRT1 and ZNF350 levels were significantly higher in OP samples than in normal samples. SIRT1 and ZNF350 are important transcriptional regulatory factors for the pathogenesis of OP and may be novel biomarkers for OP treatment.

The novel candidate gene Grb10 regulates the growth performance of Guizhou white goats

Growth factor receptor binding protein 10 (Grb10) regulates muscle growth but its function in goats is not well studied. This study examined the relationship between Grb10 gene polymorphism and growth traits in Guizhou white goats. Further, the effect of promoter polymorphism on Grb10 transcription was analyzed via a dual-luciferase assay. Quantitative reverse transcription-polymerase chain reaction analysis showed that the expression level of the Grb10 gene was the highest in the longissimus dorsi muscle (P < 0.01) and the lowest in the spleen. Moreover, sequencing results showed that the Grb10 gene had five single nucleotide polymorphisms. The association analysis showed that g.–246 C > T, g.72323 T > C, and g.178634 A > G loci were significantly associated with growth traits (P < 0.05). Linkage disequilibrium analysis of each locus showed that g.72323 T > C and g.72814 T > A loci had the strongest linkage (r2 = 0.482, D' = 0.73). Furthermore, according to an analysis conducted using TFDB4 software, it was predicted that a mutation in the promoter region of the g.–246 C > T locus resulted in the absence of four transcriptional regulatory factors. The results of dual-luciferase reporter assay further demonstrated that mutation of the g.–246 C > T locus reduced the transcriptional activity of the promoter region of the Grb10 gene. These findings suggest that Grb10 gene polymorphism could affect growth traits in goats.