Mechanisms and biotechnological applications of transcription factors

Hepatocyte Nuclear Factor 4 Alpha: A Key Regulator of Liver Disease Pathology and Haemostatic Disorders

OBJECTIVE

Hepatocyte nuclear factor 4 alpha (HNF4α) is a master regulator of hepatocyte differentiation in fetal and adult liver and exerts its transcriptional role in determining physiological functions of the liver. The objective of this review is to address the current knowledge of molecular mechanisms involved in HNF4α regulation in multiple aspects of liver disease pathogenesis.

METHODS

Based on available literature, this review summarises the current state of knowledge onthe mechanism of HNF4α dysregulation, and the role of HNF4α activity inregulating early to advanced stages of various liver diseases.

RESULTS

Patients with deranged HNF4α expression are at higher risk for the development of liver diseases such as viral hepatitis, alcoholic/nonalcoholic fatty liver disease, hepatocellular carcinoma, and haematological disorders such as coagulopathy and bleeding disorders.

DISCUSSION

HNF4α interactions with nuclear receptors and target genes promote liver disease pathology by regulating various metabolic pathways. The strong correlation between deranged HNF4α expression and the severity of liver diseases suggests that targeting HNF4α expression can offer potential therapeutic strategy in the prevention of liver disease pathology and haemostatic disorders.

Exploring the promoter regions of cancer predisposition genes in patients with triple-negative breast cancer reveals the presence of rare germline variants

BACKGROUND

Current genetic screening for predisposition to breast cancer (BC) is limited to BRCA1/2 exons and intron/exon boundaries, and limited information exists about the impact of variants in BRCA1/2 non-coding regions. The majority of alterations identified in these regions remain unclassified, but evidence of the impact of variants in the regulatory regions on cancer risk and response to treatment is emerging.

PATIENTS AND METHODS

This project aimed to investigate the prevalence of germline variants in the non-coding regulatory regions of BRCA1/2 and other BC predisposition genes in patients with triple-negative BC (TNBC) selected for age at cancer diagnosis and/or family history of cancer. The study also aims to investigate the relationship between these variants and clinical outcomes such as overall survival, disease-free survival (DFS), and response to treatment. We analyzed a Next-Generation Sequencing (NGS) custom panel of promoter regions of 28 genes involved in BC predisposition on 144 patients with TNBC previously tested wild type for coding regions of BRCA1/2.

RESULTS

The NGS analysis identified 635 rare variants in promoter regions of the 28 genes. Among the 144 patients, for 75 with available clinical data, rare germline variants in BRCA2 promoter were statistically significantly related to worse overall survival (OS) (P-value = .017). No differences in DFS and OS were found for the other genes. Rare variants in the CDH1 promoter were related to the highest percentage of non-pathological complete response after neoadjuvant chemotherapy (P = .0273); MLH1 and PALB2 rare non-coding variants were found to be both related to bilateral BC (P = .0146 and P = .0005, respectively) and ATM promoter variants were associated with a positive family history (P = .041).

CONCLUSION

Our results underscore the importance of searching for rare germline variants in regulatory regions of cancer predisposition genes in patients with TNBC, since these variants can be associated with an increased cancer risk.

Green tea polyphenol epigallocatechin-3-gallate mediates an antioxidant response via Nrf2 pathway in heat-stressed poultry: A review

Heat stress is a critical challenge in the poultry industry. It arises when birds are exposed to elevated ambient temperatures beyond their thermoneutral zone, often exacerbated by high humidity and inadequate ventilation. This condition disrupts the birds' ability to maintain thermal homeostasis, leading to physiological and behavioral changes such as increased panting, reduced feed intake, and elevated water consumption. These responses aim to dissipate heat but often result in energy imbalances, oxidative stress, and impaired immune function. Green tea polyphenols (GTPs) mitigate heat stress in poultry birds by modulating oxidative stress pathways, primarily by scavenging reactive oxygen species (ROS) and enhancing antioxidant defense mechanisms. These pathways play a pivotal role in neutralizing ROS generated during oxidative stress, inflammation, and exposure to electrophilic compounds. This action helps restore cellular balance and enhances overall antioxidant defense mechanisms by converting harmful free radicals into less reactive molecules, such as water and oxygen. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) plays a significant character in the activation of the enzymatic antioxidants network. It translocates to the nucleus upon activation, binds to antioxidant response elements (AREs) in the promoter regions of target genes, and upregulates the expression of key antioxidant enzymes. Therefore, the regulation of Nrf2 is considered a critical molecular marker in mitigating the effects of heat stress, as its activation enhances the expression of antioxidant and detoxification enzymes, protecting against oxidative damage and inflammation induced by elevated temperatures. This exploratory review summarizes the antioxidant mechanisms and anti-oxidative stress effects of GTPs in mitigating heat stress in poultry. It highlights the cytoprotective molecular basis of epigallocatechin-3-gallate (EGCG), particularly its role in modulating Nrf2-mediated cellular pathways, which enhance antioxidant defense systems and protect against oxidative damage.

RNA-Seq of Chicken Embryo Liver Reveals Transcriptional Pathways Influenced by Egg Formaldehyde Treatment

BACKGROUND/OBJECTIVES

Hatchery fumigation is recognized as a crucial step to control microbial bloom in the environment, and formaldehyde is one of the most widely used disinfectants to ensure successful hatchability and healthy production. While many of the benefits are thought to be derived from disinfectant properties, it is possible that additional host gene and genetic pathway modulation could contribute to these outcomes. The current study aimed to capture the in ovo transcriptional response of liver tissue to formaldehyde treatment.

METHODS

Chick embryos were subjected to formaldehyde fumigation treatment for 25 min at 24-25 °C and 75% relative humidity, keeping a control group as untreated. On the 18th day of incubation at 37.8 °C and 58-63% humidity, eggs were broken, and liver tissue was obtained for RNA isolation, cDNA library preparation, and RNA sequencing.

RESULTS

Bioinformatics analysis revealed 908 significant differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. A total of 672 DEGs were upregulated, whereas 236 genes were downregulated in response to FA treatment. Of the 94 novel genes, 80 were upregulated. Key DEGs, associated QTLs, and transcription factors were involved in immuno-inflammatory responses, oxidative stress, epigenetic modification, and cellular adaptation-related activities. Further research should focus on biological validation of key DEGs to clarify their roles, pathways, and relationships to FA treatment.

CONCLUSIONS

Overall, these findings (1) provide critical molecular detail as a first step towards genetic selection to improve formaldehyde treatment response and effectiveness, and (2) provide DEG signatures for FA treatment as a reference against which to compare other interventions to achieve hatchability and production benefits.

Geniposide protects against cerebral ischemic injury by targeting SOX2/RIPK1 axis

Convincing evidence has indicated that geniposide possesses neuroprotective effects in ischemic stroke. This study is designed to explore the potential molecular mechanism of geniposide in oxygen-glucose deprivation/reoxygenation (OGD/R)-treated BV-2 microglial cells and middle cerebral artery occlusion (MCAO) mice. OGD/R model in BV2 microglial cells was established in this research. Cell viability and apoptosis were determined using Cell Counting Kit-8 (CCK-8) and flow cytometry assays. Protein levels of B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), microtubule-associated protein light chain 3 (LC3)-II/LC3-I, Beclin-1, inducible nitric oxide synthase (iNOS), CD86, sex determining region Y-box 2 (SOX2), receptor-interacting serine/threonine-protein kinase 1 (RIPK1), TNF-α, IL-1β, ARG1, and CD163 were detected by western blot assay. RIPK1 mRNA level was determined using real-time quantitative polymerase chain reaction (RT-qPCR). TNF-α and IL-1β levels were analyzed using ELISA kits. After JASPAR analysis, binding between SOX2 and RIPK1 promoter was predicted and verified using chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays. The effects of geniposide on cerebral ischemic injury were assessed using MCAO mice in vivo. Geniposide treatment relieved OGD/R-triggered BV-2 cell viability promotion and apoptosis, autophagy, inflammatory response, and M1 polarization inhibition in vitro. SOX2 and RIPK1 expression was decreased in OGD/R-treated BV-2 cells. In mechanism, SOX2 upregulated RIPK1 transcription by binding to the RIPK1 promoter region. Geniposide administration significantly alleviated cerebral ischemic injury in MCAO mice in vivo. Geniposide administration protects against cerebral ischemic injury through regulating the SOX2/RIPK1 axis, providing a potential direction for the application of geniposide in the treatment of ischemic stroke.

FOXOs and their roles in acute and chronic neurological disorders

The forkhead family of transcription factors of class O (FOXOs) consisting of four functionally related proteins, FOXO1, FOXO3, FOXO4, and FOXO6, are mammalian homologs of daf-16 in Caenorhabditis elegans and were previously identified as tumor suppressors, oxidative stress sensors, and cell survival modulators. Under normal physiological conditions, FOXO protein activities are negatively regulated by phosphorylation via the phosphoinositide 3-kinase (PI3K)-Akt pathway, a well-known cell survival pathway: Akt phosphorylates FOXOs to inactivate their transcriptional activity by relocalizing FOXOs from the nucleus to the cytoplasm for degradation. However, under oxidative stress or absent the cellular survival drive of growth factors, FOXO proteins translocate to the nucleus and upregulate a series of target genes, thereby promoting cell growth arrest and cell death and altering mitochondrial homeostasis. FOXO gene expression is also regulated by other transcriptional factors such as p53 or autoregulation by their activities and end products. Here we summarize the structure, posttranslational modifications, and translocation of FOXOs linking to their transcriptional control of cellular functions, survival, and death, emphasizing their role in regulating the cellular response to some acute insults and chronic neurological disorders. This review will conclude with a brief section on potential therapeutic interventions that can be used to modulate FOXOs' activities when treating acute and chronic neurological disorders.

Plant secondary metabolites against biotic stresses for sustainable crop protection

Sustainable agriculture practices are indispensable for achieving a hunger-free world, especially as the global population continues to expand. Biotic stresses, such as pathogens, insects, and pests, severely threaten global food security and crop productivity. Traditional chemical pesticides, while effective, can lead to environmental degradation and increase pest resistance over time. Plant-derived natural products such as secondary metabolites like alkaloids, terpenoids, phenolics, and phytoalexins offer promising alternatives due to their ability to enhance plant immunity and inhibit pest activity. Recent advances in molecular biology and biotechnology have improved our understanding of how these natural compounds function at the cellular level, activating specific plant defense through complex biochemical pathways regulated by various transcription factors (TFs) such as MYB, WRKY, bHLH, bZIP, NAC, and AP2/ERF. Advancements in multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, have significantly improved the understanding of the regulatory networks that govern PSM synthesis. These integrative approaches have led to the discovery of novel insights into plant responses to biotic stresses, identifying key regulatory genes and pathways involved in plant defense. Advanced technologies like CRISPR/Cas9-mediated gene editing allow precise manipulation of PSM pathways, further enhancing plant resistance. Understanding the complex interaction between PSMs, TFs, and biotic stress responses not only advances our knowledge of plant biology but also provides feasible strategies for developing crops with improved resistance to pests and diseases, contributing to sustainable agriculture and food security. This review emphasizes the crucial role of PSMs, their biosynthetic pathways, the regulatory influence of TFs, and their potential applications in enhancing plant defense and sustainability. It also highlights the astounding potential of multi-omics approaches to discover gene functions and the metabolic engineering of genes associated with secondary metabolite biosynthesis. Taken together, this review provides new insights into research opportunities for enhancing biotic stress tolerance in crops through utilizing plant secondary metabolites.

Predicting TF-Target Gene Association Using a Heterogeneous Network and Enhanced Negative Sampling

Identifying interactions between transcription factors (TFs) and target genes is crucial for understanding the molecular mechanisms involved in biological processes and diseases. Traditional biological experiments used to determine these interactions are often time-consuming, costly, and limited in scale. Current computational methods mainly predict binding sites rather than direct interactions. Although recent studies have achieved high performance in predicting TF-target gene associations, they still face a significant challenge related to constructing a robust dataset of positive and negative samples. Currently, methods do not adequately focus on selecting negative samples, resulting in incomplete coverage of potential TF-target gene relationships. This article proposes a method to select enhanced negative samples to improve the prediction performance of TF-target gene interactions. Experimental results show that the proposed method achieves an average area under the curve (AUC) value of 0.9024 ± 0.0008 through 5-fold cross-validation. These results demonstrate the model's high efficiency and accuracy, confirming its potential application in predicting TF-target gene interactions across various datasets and paving the way for large-scale biomedical research.

Genome-Wide Investigation of MADS-Box Genes in Flower Development and Environmental Acclimation of Lumnitzera littorea (Jack) Voigt

Lumnitzera littorea (Jack) Voigt is an endangered mangrove species in China. Low fecundity and environmental pressure are supposed to be key factors limiting the population expansion of L. littorea. Transcription factors with the MADS-box domain are crucial regulators of plant flower development, reproduction, and stress response. In this study, we performed a comprehensive investigation into the features and functions of MADS-box genes of L. littorea. Sixty-three LlMADS genes with similar structure and motif composition were identified in the L. littorea genome, and these genes were unevenly distributed on the 11 chromosomes. Segmental duplication was suggested to make a main contribution to the expansion of the LlMADS gene family. Some LIMADS genes exhibited differential expression in different flower types or in response to cold stress. Overexpression of the B-class gene LlMADS37 had substantial effects on the flower morphology and flowering time of transgenic Arabidopsis plants, demonstrating its key role in regulating flower morphogenesis and inflorescence. These findings largely enrich our understanding of the functional importance of MADS-box genes in the inflorescence and stress acclimation of L. littorea and provide valuable resources for future genetic research to improve the conservation of this species.

BCDB: A dual-branch network based on transformer for predicting transcription factor binding sites

Transcription factor binding sites (TFBSs) are critical in regulating gene expression. Precisely locating TFBSs can reveal the mechanisms of action of different transcription factors in gene transcription. Various deep learning methods have been proposed to predict TFBS; however, these models often need help demonstrating ideal performance under limited data conditions. Furthermore, these models typically have complex structures, which makes their decision-making processes difficult to transparentize. Addressing these issues, we have developed a framework named BCDB. This framework integrates multi-scale DNA information and employs a dual-branch output strategy. Integrating DNABERT, convolutional neural networks (CNN), and multi-head attention mechanisms enhances the feature extraction capabilities, significantly improving the accuracy of predictions. This innovative method aims to balance the extraction of global and local information, enhancing predictive performance while utilizing attention mechanisms to provide an intuitive way to explain the model's predictions, thus strengthening the overall interpretability of the model. Prediction results on 165 ChIP-seq datasets show that BCDB significantly outperforms other existing deep learning methods in terms of performance. Additionally, since the BCDB model utilizes transfer learning methods, it can transfer knowledge learned from many unlabeled data to specific cell line prediction tasks, allowing our model to achieve cross-cell line TFBS prediction. The source code for BCDB is available on https://github.com/ZhangLab312/BCDB.

Human stem cell-specific epigenetic signatures control transgene expression

Human stem cell-derived models have emerged as an important platform to study tissue differentiation and disease mechanisms. Those models could capitalize on biochemical and cell biological methodologies such as omics, autophagy, and organelle dynamics. However, epigenetic silencing in stem cells creates a barrier to apply genetically encoded tools. Here we investigate the molecular mechanisms underlying exogenously expressed gene silencing by employing multiple commonly used promoters in human induced pluripotent stem cells (iPSCs), glioblastoma cells (GBM), and embryonic kidney cells (HEK). We discover that all promoters tested are highly methylated on the CpG island regions with lower protein expression in iPSCs, as compared to non-iPSCs. Elongation factor 1 alpha short (EF1α short or EFS) promoter, which has fewer CpG island number compared to the other promoters, can drive relatively higher gene expression in iPSCs, despite CpG methylation. Adding a minimal A2 ubiquitous chromatin opening element (minimal A2 UCOE or miniUCOE) upstream of a promoter inhibits CpG methylation and enhances gene expression in iPSCs. Our results demonstrate stem cell type-specific epigenetic modification of transgenic promoter region and provide useful information for designing anti-silencing strategies to increase transgene expression in iPSCs.

BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells

Understanding cell destiny requires unraveling the intricate mechanism of gene regulation, where transcription factors (TFs) play a pivotal role. However, the actual contribution of TFs, that is TF activity, is not only determined by TF expression, but also accessibility of corresponding chromatin regions. Therefore, we introduce BIOTIC, an advanced Bayesian model with a well-established gene regulation structure that harnesses the power of single-cell multi-omics data to model the gene expression process under the control of regulatory elements, thereby defining the regulatory activity of TFs with variational inference. We demonstrated that the TF activity inferred by BIOTIC can serve as a characterization of cell identity, and outperforms baseline methods for the tasks of cell typing, cell development tracking, and batch effect correction. Additionally, BIOTIC trained on multi-omics data can flexibly be applied to the scenario where merely single-cell transcriptome sequencing is available, to infer TF activity and annotate the cell type by mapping the query cell into the reference TF activity space, as an emerging application of cell atlases. The structure of BIOTIC has been determined to be adaptable for the inclusion of additional biological factors, allowing for flexible and more comprehensive gene regulation analysis. BIOTIC introduces a pioneering biological-mechanism-driven framework to infer TF activity and elucidate cell identity states at gene regulatory level, paving the way for a deeper understanding of the complex interplay between TFs and gene expression in living systems.

Insights into the regulatory mechanisms and application prospects of the transcription factor Cra

Cra (catabolite repressor/activator) is a global transcription factor (TF) that plays a pleiotropic role in controlling the transcription of several genes involved in carbon utilization and energy metabolism. Multiple studies have investigated the regulatory mechanism of Cra and its rational use for metabolic regulation, but due to the complexity of its regulation, there remain challenges in the efficient use of Cra. Here, the structure, mechanism of action, and regulatory function of Cra in carbon and nitrogen flow are reviewed. In addition, this paper highlights the application of Cra in metabolic engineering, including the promotion of metabolite biosynthesis, the regulation of stress tolerance and virulence, the use of a Cra-based biosensor, and its coupling with other transcription factors. Finally, the prospects of Cra-related regulatory strategies are discussed. This review provides guidance for the rational design and construction of Cra-based metabolic regulation systems.

The impact of antibiotic induction on virulence and antibiotic resistance in Klebsiella pneumoniae: a comparative study of CSKP and CRKP strains

Background

Klebsiella pneumoniae is an opportunistic pathogen causing nosocomial infections, classified into carbapenem-sensitive and carbapenem-resistant strains. Understanding the virulence factors and antibiotic resistance of these strains is essential for effective clinical management.

Objective

This study compared the virulence genes and antibiotic resistance profiles of 50 CSKP and 50 CRKP strains, examining their expression under antibiotic pressure and the mechanisms contributing to their pathogenicity.

Methods

Virulence genes (rmpA, rmpA2, iucA, iutA, Peg-344, ybts, iroB) were detected in both strains using polymerase chain reaction (PCR). Antibiotic susceptibility testing established minimum inhibitory concentrations (MICs) for key antibiotics. Gene expression analysis was performed with quantitative reverse transcription PCR (qRT-PCR) after 10 days of antibiotic exposure.

Results

CSKP strains exhibited significantly higher positivity rates for virulence genes compared to CRKP strains. CRKP strains predominantly expressed resistance genes KPC, SHV, and CTX-M3, whereas no resistance genes were found in CSKP. Antibiotic susceptibility tests showed increased MICs, particularly for ciprofloxacin and imipenem, following antibiotic induction. CSKP demonstrated elevated expression of rmpA and rmpA2, while CRKP showed increased expression of SHV, and KPC after antibiotic exposure.

Conclusion

This study highlights the intricate relationship between virulence and resistance in Klebsiella pneumoniae. CSKP strains show strong virulence factor expression, while CRKP strains adapt to antibiotic pressure through altered gene expression patterns. These findings underscore the urgent need for continuous surveillance and innovative therapeutic strategies to combat multidrug-resistant Klebsiella pneumoniae infections.

The transcription factor CAMTA2 interacts with the histone acetyltransferase GCN5 and regulates grain weight in wheat

Grain weight and size are major traits targeted in breeding to improve wheat (Triticum aestivum L.) yield. Here, we find that the histone acetyltransferase GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) physically interacts with the calmodulin-binding transcription factor CAMTA2 and regulates wheat grain size and weight. gcn5 mutant grains were smaller and contained less starch. GCN5 promoted the expression of the starch biosynthesis genes SUCROSE SYNTHASE 2 (Sus2) and STARCH-BRANCHING ENZYME Ic (SBEIc) by regulating H3K9ac and H3K14ac levels in their promoters. Moreover, immunoprecipitation followed by mass spectrometry (IP-MS) revealed that CAMTA2 physically interacts with GCN5. The CAMTA2-GCN5 complex activated Sus2 and SBEIc by directly binding to their promoters and depositing H3K9ac and H3K14ac marks during wheat endosperm development. camta2 knockout mutants exhibited similar phenotypes to gcn5 mutants, including smaller grains that contained less starch. In gcn5 mutants, transcripts of high molecular weight (HMW) Glutenin (Glu) genes were downregulated, leading to reduced HMW glutenin protein levels, gluten content, and sodium dodecyl sulfate (SDS) sedimentation volume. However, the association of GCN5 with Glu genes was independent of CAMTA2, since GCN5 enrichment on Glu promoters was unchanged in camta2 knockouts. Finally, we identified a CAMTA2-AH3 elite allele that corresponded with enhanced grain size and weight, serving as a candidate gene for breeding wheat varieties with improved grain weight.

Dynamics design of a non-natural transcription factor responding to androst-4-ene-3,17-dione

The production of androst-4-ene-3,17-dione (AD) by the steroidal microbial cell factory requires transcription factors (TFs) to participate in metabolic regulation. However, microbial cell factory lacks effective TFs that can respond to AD in its metabolic pathway. Additionally, finding and obtaining natural TFs that specifically respond to AD is a complex and onerous task. In this study, we devised an artificial TF that responds to AD, termed AdT, based on structure-guided molecular dynamics (MD) simulation. According to MD analysis of the conformational changes of AdT after binding to AD, an LBD in which the N- and C-termini exhibited convergence tendencies was used as a microswitch to guide the assembly of a DNA-binding domain lexA, a linker (GGGGS)2, and a transcription activation domain B42 into an artificial TF. As a proof of design, a AD biosensor was designed and constructed in yeast on the basis of the ligand-binding domain (LBD) of hormone receptor. In addition, the transcription factor activity of AdT was increased by 1.44-fold for its variant F320Y. Overall, we created non-natural TF elements for AD microbial cell factory, and expected that the design TF strategy will be applied to running in parallel to the signaling machinery of the host cell.

Deciphering the mechanisms involved in reduced sensitivity to azoles and fengycin lipopeptide in Venturia inaequalis

Apple scab, caused by the hemibiotrophic fungus Venturia inaequalis, is currently the most common and damaging disease in apple orchards. Two strains of V. inaequalis (S755 and Rs552) with different sensitivities to azole fungicides and the bacterial metabolite fengycin were compared to determine the mechanisms responsible for these differences. Antifungal activity tests showed that Rs552 had reduced sensitivity to tebuconazole and tetraconazole, as well as to fengycin alone or in a binary mixture with other lipopeptides (iturin A, pumilacidin, lichenysin). S755 was highly sensitive to fengycin, whose activity was close to that of tebuconazole. Unlike fengycin, lipopeptides from the iturin family (mycosubtilin, iturin A) had similar activity on both strains, while those from the surfactin family (lichenysin, pumilacidin) were not active, except in binary mixtures with fengycin. The activity of lipopeptides varies according to their family and structure. Analyses to determine the difference in sensitivity to azoles (which target the CYP51 enzyme involved in the ergosterol biosynthesis pathway) showed that the reduced sensitivity in Rs552 is linked to (i) a constitutive increased expression of the Cyp51A gene caused by insertions in the upstream region and (ii) greater efflux by membrane pumps with the involvement of ABC transporters. Microscopic observations revealed that fengycin, known to interact with plasma membranes, induced morphological and cytological changes in cells from both strains. Sterol and phospholipid analyses showed a higher level of ergosta-7,22-dien-3-ol and a lower level of PI(C16:0/C18:1) in Rs552 compared with S755. These differences could therefore influence the composition of the plasma membrane and explain the differential sensitivity of the strains to fengycin. However, the similar antifungal activities of mycosubtilin and iturin A in the two strains indirectly indicate that sterols are probably not involved in the fengycin resistance mechanism. This leads to the conclusion that different mechanisms are responsible for the difference in susceptibility to azoles or fengycin in the strains studied.

6-Methyl-5-hepten-2-one promotes programmed cell death during superficial scald development in pear

Plants possess the ability to induce programmed cell death (PCD) in response to abiotic and biotic stresses; nevertheless, the evidence on PCD initiation during pear scald development and the involvement of the scald trigger 6-methyl-5-hepten-2-one (MHO) in this process is rudimentary. Pyrus bretschneideri Rehd. cv. 'Dangshansuli' pear was used to validate such hypothesis. The results showed that superficial scald occurred after 120-d chilling exposure, which accompanied by typical PCD-associated morphological alterations, such as plasmolysis, cell shrinkage, cytosolic and nuclear condensation, vacuolar collapse, tonoplast disruption, subcellular organelle swelling, and DNA fragmentation. These symptoms were aggravated after MHO fumigation but alleviated by diphenylamine (DPA) dipping. Through transcriptome assay, 24 out of 146 PCD-related genes, which were transcribed during cold storage, were identified as the key candidate members responsible for these cellular biological alternations upon scald development. Among these, PbrCNGC1, PbrGnai1, PbrACD6, and PbrSOBIR1 were implicated in the MHO signaling pathway. Additionally, PbrWRKY2, 34 and 39 could bind to the W-box element in the promoter of PbrGnai1 or PbrSOBIR1 and activate their transcription, as confirmed by dual-luciferase, yeast one-hybrid, and transient overexpression assays. Hence, our study confirms the PCD initiation during scald development and explores the critical role of MHO in this process.

Cotton Pectate Lyase GhPEL48_Dt Promotes Fiber Initiation Mediated by Histone Acetylation

GhPEL48_Dt, a Pectate lyase (PEL, EC4.2.2.2), is a crucial enzyme involved in cell-wall modification and pectin degradation. Studies have shown that the GhPEL48_Dt also plays a significant role in cotton-fiber development; however, the specific function and regulatory mechanism of GhPEL48_Dt in cotton-fiber development are still not fully understood. Here, we found that the histone deacetylase inhibitor-Trichostatin A significantly reduces the transcript levels of GhPEL48_Dt and its enzyme activity. Further, silencing of GhPEL48_Dt significantly inhibits the initiation and elongation of cotton fibers by promoting pectin degradation, and the heterologous expression of GhPEL48_Dt promotes the development of trichomes and root hairs in Arabidopsis, which suggests that GhPEL48_Dt plays a positive and conserved role in single cell i.e., fiber, root hair, and leaf trichome development. Collectively, this paper provides a comprehensive analysis of the fundamental characteristics and functions of GhPEL48_Dt in fiber development, including the regulatory role of histone acetylation on GhPEL48_Dt, which contributes to the understanding of pectin degradation pathways and establishes a theoretical foundation for elucidating its regulatory mechanism.

TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor-Target Interactions

Transcription factors (TFs) are crucial in modulating gene expression and sculpting cellular and organismal phenotypes. The identification of TF-target gene interactions is pivotal for comprehending molecular pathways and disease etiologies but has been hindered by the demanding nature of traditional experimental approaches. This paper introduces a novel web application and package utilizing the R program, which predicts TF-target gene relationships and vice versa. Our application integrates the predictive power of various bioinformatic tools, leveraging their combined strengths to provide robust predictions. It merges databases for enhanced precision, incorporates gene expression correlation for accuracy, and employs pan-tissue correlation analysis for context-specific insights. The application also enables the integration of user data with established resources to analyze TF-target gene networks. Despite its current limitation to human data, it provides a platform to explore gene regulatory mechanisms comprehensively. This integrated, systematic approach offers researchers an invaluable tool for dissecting the complexities of gene regulation, with the potential for future expansions to include a broader range of species.

The effect of exogenous melatonin on waterlogging stress in Clematis

Clematis is the queen of the vines, being an ornamental plant with high economic value. Waterlogging stress reduces the ornamental value of the plant and limits its application. Melatonin plays an important role in plant resistance to abiotic stresses. In this study, the physiological responses and gene expression levels of two wild species, namely, Clematis tientaiensis and Clematis lanuginosa, and two horticultural varieties, namely, 'Sen-No-Kaze' and 'Viva Polonia,' under waterlogging stress were analyzed to determine the effect of melatonin on waterlogging tolerance. The results showed that the waterlogging tolerances of C. lanuginosa and 'Sen-No-Kaze' were relatively poor, but were significantly improved by concentrations of 100 μmol·L-1 and 50 μmol·L-1 melatonin. C. tientaiensis and 'Viva Polonia' had relatively strong tolerance to waterlogging, and this was significantly improved by 200 μmol·L-1 melatonin. Under waterlogging stress, the relative conductivity and H2O2 content of Clematis increased significantly; the photosynthetic parameters and chlorophyll contents were significantly decreased; photosynthesis was inhibited; the contents of soluble protein and soluble sugars were decreased. Effective improvement of waterlogging tolerance after exogenous melatonin spraying, the relative conductivity was decreased by 4.05%-27.44%; the H2O2 content was decreased by 3.84%-23.28%; the chlorophyll content was increased by 35.59%-103.36%; the photosynthetic efficiency was increased by 25.42%-45.86%; the antioxidant enzyme activities of APX, POD, SOD, and CAT were increased by 28.03%-158.61%; the contents of proline, soluble protein, and soluble sugars were enhanced, and cell homeostasis was improved. Transcription sequencing was performed on wild Clematis with differences in waterlogging tolerance, and nine transcription factors were selected that were highly correlated with melatonin and that had the potential to improve waterlogging tolerance, among which LBD4, and MYB4 were significantly positively correlated with the antioxidant enzyme system, and bHLH36, DOF36, and WRKY4 were significantly negatively correlated. Photosynthetic capacity was positively correlated with DOF36 and WRKY4 while being significantly negatively correlated with MYB4, MOF1, DOF47, REV1 and ABR1. Melatonin could enhance the flooding tolerance of Clematis by improving photosynthetic efficiency and antioxidant enzyme activity. This study provides an important basis and reference for the application of melatonin in waterlogging-resistant breeding of Clematis.

Transcription factor-based biosensor: A molecular-guided approach for advanced biofuel synthesis

As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental protection. Traditional engineering of cell factories for production of advanced biofuels lacks efficient high-throughput screening tools and regulating systems, impeding the improvement of cellular productivity and yield. Transcription factor-based biosensors have been widely applied to monitor and regulate microbial cell factory products due to the advantages of fast detection and in-situ screening. This review updates the design and application of transcription factor-based biosensors tailored for advanced biofuels and related intermediates. The construction and genetic parts selection principle of biosensors are discussed. Strategies to enhance the performance of biosensor, including regulating promoter strength and RBS strength, optimizing plasmid copy number, implementing genetic amplifier, and modulating the structure of transcription factor, have also been summarized. We further review the application of biosensors in high-throughput screening of new metabolic engineering targets, evolution engineering, confirmation of protein function, and dynamic regulation of metabolic flux for higher production of advanced biofuels. At last, we discuss the current limitations and future trends of transcription factor-based biosensors.

Strategies to increase the robustness of microbial cell factories

Engineering microbial cell factories have achieved much progress in producing fuels, natural products and bulk chemicals. However, in industrial fermentation, microbial cells often face various predictable and stochastic disturbances resulting from intermediate metabolites or end product toxicity, metabolic burden and harsh environment. These perturbances can potentially decrease productivity and titer. Therefore, strain robustness is essential to ensure reliable and sustainable production efficiency. In this review, the current strategies to improve host robustness were summarized, including knowledge-based engineering approaches, such as transcription factors, membrane/transporters and stress proteins, and the traditional adaptive laboratory evolution based on natural selection. Computation-assisted (e.g. GEMs, deep learning and machine learning) design of robust industrial hosts was also introduced. Furthermore, the challenges and future perspectives on engineering microbial host robustness are proposed to promote the development of green, efficient and sustainable biomanufacturers.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.