Promoter Region Of Gene Research Articles

Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs

Bladder cancer (BC) is a malignant tumor characterized by a high incidence of urinary system diseases. The complex pathogenesis of BC has long been a focal point in medical research. With the robust development of epigenetics, the crucial role of epigenetic modifications in the occurrence and progression of BC has been elucidated. These modifications not only affect gene expression but also impact critical biological behaviors of tumor cells, including proliferation, differentiation, apoptosis, invasion, and metastasis. Notably, DNA methylation, an important epigenetic regulatory mechanism, often manifests as global hypomethylation or hypermethylation of specific gene promoter regions in BC. Alterations in this methylation pattern can lead to increased genomic instability, which profoundly influences the expression of proto-oncogenes and tumor suppressor genes. MiRNAs, as noncoding small RNAs, participate in various biological processes of BC by regulating target genes. Consequently, this work aims to explore the interaction mechanisms between DNA methylation and miRNAs in the occurrence and development of BC. Research has demonstrated that DNA methylation not only directly influences the expression of miRNA genes but also indirectly affects the maturation and functionality of miRNAs by modulating the methylation status of miRNA promoter regions. Simultaneously, miRNAs can regulate DNA methylation levels by targeting key enzymes such as DNA methyltransferases (DNMTs), thereby establishing a complex feedback regulatory network. A deeper understanding of the crosstalk mechanisms between DNA methylation and miRNAs in BC will contribute to elucidating the complexity and dynamics of epigenetic modifications in this disease, and may provide new molecular targets and strategies for the early diagnosis, treatment, and prognostic evaluation of BC.

Molecular analysis of AmpC-producing Escherichia coli isolated from pediatric patients.

AmpC-mediated cephalosporin resistance occurs in 1.0% to 3.3% of Escherichia coli isolates due to production of either plasmid-mediated AmpC (p-AmpC) or chromosomal AmpC (c-AmpC). Data on the prevalence and molecular characteristics of AmpC-producing E. coli in pediatric patients are limited. We analyzed E. coli clinical strains with resistance phenotype consistent with AmpC production isolated from patients at a pediatric hospital in Japan between 2015 and 2022. Sequence types, resistance genes, and relevant mutations were identified through whole genome sequencing. Promoter and attenuator regions of the chromosomal ampC gene were examined and the presence of plasmid-mediated ampC genes was determined. Among 2,081 E. coli strains, 80 (3.8%) from 27 patients demonstrated the AmpC phenotype. The median patient age was 55 months, with 92.6% having underlying diseases, mainly renal and urinary tract abnormalities. Of the 27 strains, p-AmpC was found in 9 strains including 6 strains belonging to ST131, while c-AmpC was identified in 18 strains including 9 ST73 strains and 4 ST12 strains. ST131 and ST73 were the major AmpC-E. coli lineages isolated from children with underlying diseases. Most ST131 strains harbored p-ampC, while all ST73 strains acquired cephalosporin resistance by c-AmpC production through promoter and attenuator mutations, suggesting the presence of both AmpC mechanisms in a lineage-specific manner in E. coli identified among hospitalized children.

Identification of a central regulator of ginkgolide biosynthesis in Ginkgo biloba that integrates jasmonate and light signaling

Ginkgolides are secondary metabolites unique to Ginkgo biloba with the potential to prevent and treat cardiovascular and cerebrovascular diseases. Although the biosynthetic pathways of ginkgolides have been partly uncovered, the mechanism regulating their biosynthesis is still largely unknown. Here, using multiomic and genetic analyses, we report the identification of a transcription factor, named ETHYLENE RESPONSE FACTOR ASSOCIATED WITH GINKGOLIDE BIOSYNTHESIS (GbEAG), as a critical regulator of ginkgolide biosynthesis. GbEAG is highly expressed in the roots of G. biloba, and its expression is significantly induced by methyl jasmonate (MeJA). Ginkgolide content was significantly increased in roots by overexpressing GbEAG using a "cut-dip-regeneration" system. GbEAG positively regulates ginkgolide biosynthesis by directly binding to the GCC-boxes in the promoter regions of genes involved in the biosynthesis of ginkgolides, such as ISOPENTENYL DIPHOSPHATE ISOMERASE (GbIDI) and CYTOCHROME P450 7005C3 (GbCYP7005C3). GbEAG mediates the jasmonic acid (JA)-activated ginkgolide synthesis through its direct interaction with the JASMONATE ZINC-FINGER INFLORESCENCE MERISTEM DOMAIN 3 (GbJAZ3) repressor. Importantly, we also found that the central light-response regulator ELONGATED HYPOCOTYL 5 (GbHY5) mediates light induction of ginkgolide biosynthesis by binding to the G-box in the GbEAG promoter. Our findings provide mechanistic insights into the coordinated regulation of ginkgolide biosynthesis via JA and light signals, with GbEAG as a central regulator in G. biloba, and shed light on the potential to develop ginkgolide-rich varieties through molecular breeding and gene editing.

Genome-wide identification and comprehensive analysis of the FtsH gene family in wheat.

The filamentation temperature-sensitive H (FtsH) gene family, which is known to play a critical role in plant growth and development by regulating photosynthesis, chloroplast development, and response to plant stress, has been extensively studied in various species. However, the FtsH gene family in wheat has not been previously documented. In this study, 38 TaFtsH gene family members were identified, divided into eight groups and unevenly distributed across various chromosomes. Analysis of gene structure and conserved motifs revealed that TaFtsH genes within the same taxon share similar gene structures and conserved motifs. Further collinearity analysis provided insights into the evolutionary history of TaFtsH genes. Examination of cis-acting elements in the promoter region of TaFtsH genes revealed the presence of developmental and stress response elements in genes. The expression pattern of the wheat FtsH gene under various abiotic stresses was analyzed using real-time fluorescence quantitative PCR. Additionally, transient expression in tobacco verified the localization of the TaFtsH11-B protein in chloroplasts. These findings collectively contribute to laying the groundwork for the functional characterization of TaFtsH genes.

Excessive MYC Orchestrates Macrophages induced Chromatin Remodeling to Sustain Micropapillary-Patterned Malignancy in Lung Adenocarcinoma.

Current understanding of micropapillary (MP)-subtype lung adenocarcinoma (LUAD) remains confined to biological activities and genomic landscapes. Unraveling the major regulatory programs underlying MP patterned malignancy offers opportunities to identify more feasible therapeutic targets for patients with MP LUAD. This study shows that patients with MP subtype LUAD have aberrant activation of the MYC pathway compared to patients with other subtypes. In vitro and xenograft mouse model studies reveal that MP pattern in malignancy cannot be solely due to aberrant MYC expression but requires the involvement of M2-like macrophages. Excessively expressed MYC leads to the accumulation of M2-like macrophages from the bone marrow, which secretes TGFβ, to induce the expression of FOSL2 in tumor cells, thereby remodeling chromatin accessibility at promoter regions of MP-pattern genes to promote the MYC-mediated de novo transcriptional regulation of these genes. Additionally, the MP-pattern in malignancy can be effectively alleviated by disrupting the TGFβ-FOSL2 axis. These findings reveal new functions for the M2-like macrophage-TGFβ-FOSL2 axis in MYC-overexpressing MP-subtype LUAD, identifying targetable vulnerabilities in this pathway.

Echinocandin Adaptation in Candida albicans Is Accompanied by Altered Chromatin Accessibility at Gene Promoters and by Cell Wall Remodeling

Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well as mechanisms involving induced aneuploidy, that can govern this. Still, the mechanisms of ECN adaptation are not fully understood. Here, we use genome-wide profiling of chromatin accessibility by ATAC-seq to determine if ECN adaptation is reflected in changes in the chromatin landscape in the absence of aneuploidy. We find that drug adaptation is coupled with multiple changes in chromatin accessibility genome-wide, which occur predominantly in gene promoter regions. Areas of increased accessibilities in promoters are enriched with the binding motifs for at least two types of transcription factors: zinc finger and basic leucine zipper. We also find that chromatin changes are often associated with differentially expressed genes including genes with functions relevant to the ECN-adapted phenotype, such as cell wall biosynthesis. Consistent with this, we find that the cell wall is remodeled in ECN-adapted mutants, with chitin up and glucan down and increased cell surface exposure. A full understanding of ECN adaptation processes is of critical importance for the prevention of clinical resistance.

FOXP1 is a Transcription Factor for the Alzheimer's Disease Risk Gene SORL1.

Sortilin-related receptor 1 (SORL1) is a risk gene of Alzheimer's disease (AD), and some protein-truncating (PTV) and rare missense variants causing the loss of function of SORL1 contribute to AD pathogenesis. SORL1 is an endosomal receptor that interacts with multiple protein sorting complexes to facilitate the transport of various cargoes through the endolysosomal network (ELN). However, the regulatory mechanisms governing SORL1 expression remain unknown. Through biochemical methods, we identified Forkhead Box P1 (FOXP1) as a binding protein to the minimal promoter region of SORL1 gene. Silencing FOXP1 using siRNA significantly decreased the activity of the SORL1 minimal promoter and reduced SORL1 protein and mRNA levels in the neuroblastoma cell line SH-SY5Y. Additionally, using 5xFAD mouse models of AD, we observed significantly decreased FOXP1 and SORL1 expression in neurons within the prefrontal cortex. Disruption of ELN and the autophagy degradation system by bafilomycin A1 (BafA1) appeared to be a specific condition to suppress FOXP1 and hence SORL1 in SH-SY5Y cells. These findings highlight the critical role of FOXP1 in regulating SORL1 expression and suggest that FOXP1 could be a potential target to maintain SORL1 expression for AD prevention and therapy.

Characterization of a heat shock factor 1 (HSF1) gene and the association of its single nucleotide polymorphisms with susceptibility/resistance of Magallana gigas to Halomonas sp. 7T.

Heat shock transcription factor 1 (HSF1) is an important activator of innate immunity in the response of invertebrates to pathogen invasion. In the present study, a HSF1 was characterized in Pacific oyster Magallana gigas (MgHSF1), and its association of single nucleotide polymorphisms with susceptibility/resistance of oyster to Halomonas sp. 7T were investigated. MgHSF1 shared highly conserved DNA binding and acetylation sites with other organisms. The MgHSF1 mRNA showed high expression in haemocytes, and was significantly induced by lipopolysaccharide stimulation. The single nucleotide polymorphisms (SNPs) within promoter region of MgHSF1 gene from two oyster populations (the bacterial-resistant population and the common population) were investigated to analyze their association with bacterial resistance. Nine out of 14 SNPs including -543 A/G, -494 C/T, -488 T/A, -476 G/A, -336 C/T, -335 T/C, -334 C/T, -307 T/C and -268 T/C were found to be associated with bacterial resistance. Moreover, haplotypes TCTCGA was associated with bacterial resistance. The results threw lights on the molecular mechanisms of different oyster populations' resistance to bacterial diseases which suggested that the increased bacterial resistance of bacterial-resistant population was associated with the higher expression of MgHSF1. Meanwhile, the nine genotypes (-543 G/G, -494 T/T, -488 A/A, -476 A/A, -336 T/T, -335 C/C, -334 T/T, -307 T/T, and -268 C/C) and one haplotype (TCTCGA) could be used as potential markers for oyster selection breeding with higher bacterial resistance.

CBX2 suppresses interferon signaling to diminish tumor immunogenicity via a noncanonical corepressor complex

Chromobox 2 (CBX2), a crucial component of the polycomb repressive complex (PRC), has been implicated in the development of various human cancers. However, its role in the regulation of tumor immunogenicity and immune evasion remains inadequately understood. In this study, we found that ablation of CBX2 led to tumor growth inhibition, activation of the tumor immune microenvironment, and enhanced therapeutic efficacy of anti-PD1 or adoptive T cell therapies by using murine syngeneic tumor models. By analysis of the CBX2-regulated transcriptional program coupled with mass spectrometry screening of CBX2-interacting proteins, we found that CBX2 suppresses interferon signaling independent of its function in the canonical PRC. Mechanistically, CBX2 directly interacts with RACK1 and facilitates the recruitment of HDAC1, which attenuates the H3K27ac modification on the promoter regions of interferon-stimulated genes, thereby suppressing interferon signaling. Consequently, CBX2 reduces tumor immunogenicity and enables immune evasion. Moreover, a high expression level of CBX2 is associated with immune suppressive tumor microenvironment and reduced efficacy of immunotherapy across various human cancer types. Our study identifies a noncanonical CBX2-RACK1-HDAC1 corepressor complex in suppression of tumor immunogenicity, thereby presenting a potential target and biomarker for tumor immunotherapy.

The Potential Role of Brassica napus Metallothioneins in Salt Stress and Interactions with Plant Growth-Promoting Bacteria

Background/Objectives: Plant metallothioneins (MTs) are low-molecular-weight proteins involved in heavy metal binding and response to stress conditions. This work aimed to analyse canola (Brassica napus L.) MTs (BnMT1-4) response to salinity and plant interaction with bacteria. Methods: (1) We tested germination and canola growth and development in the presence of sodium chloride and bacteria Serratia plymuthica; (2) We analysed phytohormones content using LC-MS/MS; (3) We identified in silico cis-regulatory elements in promoters of BnMT1-4 genes; and (4) we investigated BnMT1-4 genes’ expression in B. napus. Results: Under saline conditions, canola germination and plant growth were notably inhibited, whereas inoculation of seeds with S. plymuthica significantly stimulated the analysed physiological traits of B. napus. The content of auxin, abscisic acid, jasmonates, gibberellins, and salicylic acid in B. napus was significantly affected by salinity and modulated by S. plymuthica presence. The promoter regions of the BnMT1-4 genes contain numerous regulatory elements controlled by light, hormones, and various stresses. Interestingly, the expression of BnMT1-3 genes was down-regulated under salt stress, while BnMT4 transcript levels increased strongly at the highest salt concentrations with and without S. plymuthica present. Conclusions: The results show that BnMT genes are differently affected by salinity and bacteria S. plymuthica and significantly correlate with particular phytohormones content in canola tissues, confirming the diversified functions of MTs in plant responses to changing environment.

Molecular epidemiology of β-lactamases in ceftriaxone-resistant Enterobacterales bloodstream infections in the mid-Atlantic United States.

Ceftriaxone-resistant Enterobacterales remain a public health threat; contemporary data investigating their molecular epidemiology are limited. Five hundred consecutive ceftriaxone-resistant (MIC ≥ 4 µg/mL) Enterobacterales bloodstream isolates were collected between 2018 and 2022 from three Maryland hospitals. Broth microdilution confirmed antibiotic susceptibilities. Whole-genome sequencing identified extended-spectrum β-lactamase (ESBL) and ampC genes both in bacterial chromosomes (c-ampC) and on plasmids (p-ampC). Mutations in promoter or attenuator regions of the Escherichia coli c-ampC gene (i.e., blaEC gene) with the potential to result in ampC derepression were investigated. The presence of ESBL or ampC genes was confirmed in 497 (99.4%) isolates. Two hundred seventy-nine (55.8%) isolates had both ESBL and ampC genes. ESBL families were identified among 398 (80%) patients: blaCTX-M (n = 370), blaSHV (n = 17), blaOXY (n = 14), and blaVEB (n = 5). Ceftriaxone-resistant Enterobacterales species carrying ESBL genes included the following: E. coli (67%), Klebsiella pneumoniae (24%), Klebsiella oxytoca (4%), Proteus mirabilis (2%), Enterobacter cloacae complex (2%), Klebsiella aerogenes (1%), Providencia stuartii (<1%), and Serratia marcescens (<1%). c-ampC genes were identified in 374 (75%) of the 500 isolates. Only 7% of E. coli isolates with mutations in the promoter or attenuator region of the c-ampC gene exhibited resistance to cefoxitin, a proxy for increased AmpC production. Two p-ampC genes were confirmed in 25 (5%) of the 500 isolates: blaCMY-59 (72%) and blaDHA-1 (28%; confined to E. coli [92%] and K. pneumoniae [8%]). Until comprehensive β-lactamase molecular testing is available, the species-specific prevalence of ESBL and ampC genes in ceftriaxone-resistant Enterobacterales should be considered to promote effective albeit judicious antibiotic prescribing. Mutations in promoter or attenuator regions of the E. coli c-ampC gene do not appear to contribute significantly to increased AmpC production in this species.

Genome-wide identification of the Sec14 gene family and the response to salt and drought stress in soybean (Glycine max)

BackgroundThe Sec14 domain is an ancient lipid-binding domain that evolved from yeast Sec14p and performs complex lipid-mediated regulatory functions in subcellular organelles and intracellular traffic. The Sec14 family is characterized by a highly conserved Sec14 domain, and is ubiquitously expressed in all eukaryotic cells and has diverse functions. However, the number and characteristics of Sec14 homologous genes in soybean, as well as their potential roles, remain understudied.ResultsIn this study, we identified 77 Sec14 genes in the soybean genome that were unevenly distributed across 19 chromosomes. Based on the classification method used for Arabidopsis Sec14 members, GmSec14s can be categorized into three classes: GmPITP1 to GmPITP37, GmSFH1 to GmSFH25, and GmPATL1 to GmPATL15. Structural analysis of the GmSec14 genes revealed that the SFH subfamily contained more introns than the other subfamilies. A total of 10 conserved protein motifs were detected within GmSec14 proteins, with each subfamily possessing unique motifs. Two tandem duplications and 73 segmental duplications were identified among the GmSec14 genes. Additionally, a large number of cis-acting elements, particularly those related to plant hormones, were abundant in the promoter regions of the GmSec14 genes. Tissue expression analysis of the GmSec14 genes indicated that they exhibited distinct tissue-specific expression patterns. In response to salt stress, multiple genes were found to be either upregulated or downregulated. In contrast, the majority of genes were downregulated under drought stress conditions. Notably, 12 GmSec14 genes exhibited significant alterations in expression following salt or drought stress, suggesting a potential role for these genes in stress response mechanisms. Furthermore, the protein interaction network and miRNA regulation associated with GmSec14s were predicted to elucidate the potential functions of GmSec14 members.ConclusionsThis study provides a systematic and comprehensive examination of the Sec14 gene family in soybean, which will facilitate further functional research into their roles in response to salt and drought tolerance.

IDO1 inhibits ferroptosis by regulating FTO-mediated m6A methylation and SLC7A11 mRNA stability during glioblastoma progression

Indoleamine 2, 3-dioxygenase 1 (IDO1) has been recognized as an enzyme involved in tryptophan catabolism with immunosuppressive ability. This study determined to investigate the impact of IDO1 on glioblastoma multiforme (GBM) cells. Here, we showed that the expression of IDO1 was markedly increased in patients with glioma and associated with GBM progression. IDO1 overexpression suppressed ferroptotic cell death, reduced ROS and lipid peroxide generation in GBM cells. IDO1 expression increased the SLC7A11 mRNA stability through FTO-dependent m6A methylation. Mechanistically, IDO1 promoted the AhR expression and nuclear translocation, thus facilitating AhR recruitment at the promoter regions of FTO gene and negatively regulating its transcription. These findings demonstrate that IDO1 facilitates GBM progression by inhibiting SLC7A11-dependent ferroptosis through an IDO1-AhR-FTO axis-mediated m6A methylation mechanism.

ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.

Genome-wide identification of binding profiles for DNA-binding proteins from the limited number of intracellular pathogens in infection studies is crucial for understanding virulence and cellular processes but remains challenging, as the current ChIP-exo is designed for high-input bacterial cells (>1010). Here, we developed an optimized ChIP-mini method, a low-input ChIP-exo utilizing a 5,000-fold reduced number of initial bacterial cells and an analysis pipeline, to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular Salmonella Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, elucidating changes in their binding position and binding intensity during infection. Post-infection, we observed 21 significant reductions in H-NS binding at intergenic regions, exposing the promoter region of virulence genes, such as those in Salmonella pathogenicity islands-2, 3 and effectors. Furthermore, we revealed the crucial phenomenon that novel and significantly increased RpoD bindings were found within regions exhibiting diminished H-NS binding, thereby facilitating substantial upregulation of virulence genes. These findings markedly enhance our understanding of how H-NS and RpoD simultaneously coordinate the transcription initiation of virulence genes within macrophages. Collectively, this work demonstrates a broadly adaptable tool that will enable the elucidation of DNA-binding protein dynamics in diverse intracellular pathogens during infection.

Genome-Wide Analysis, Identification, and Transcriptional Profile of the Response to Abiotic Stress of the Purple Acid Phosphatases (PAP) Gene Family in Apple

Purple acid phosphatases (PAPs) play a significant role in plant phosphorus nutrition and can not only release phosphorus from the soil but also regulate the distribution of phosphorus in plants throughout their entire growth and development process. Moreover, members of the PAP protein family exert a more extensive influence on plant mineral homeostasis, developmental processes, and stress responses. Three clusters of purple acid phosphatases, including 31 putative genes, were identified in apples (Malus domestica) by searching the Genome Database for Rosaceae. The structure, chromosomal distribution and location, phylogeny, motifs, and cis-acting elements in the gene promoter regions of the MdPAP gene family are reviewed. These genes exhibit different expression patterns in different tissues. For example, almost all MdPAP genes are strongly expressed in the roots, except for MdPAP10, MdPAP12, and MdPAP27. Similarily, all MdPAPs were expressed in the leaves while the transcript levels of MdPAP7, MdPAP10, MdPAP15, MdPAP21, MdPAP24, MdPAP26, MdPAP29, and MdPAP30 were highest in apple flowers. Overall, the expression of the 31 genes significantly changed in either the roots or leaves following the application of phosphorus and/or drought stress. These results indicate that MdPAP family members play a role in plant adaptation to adverse environments. This work explores the adaptative responses to phosphorus and/or drought conditions in apple and establishes a foundation for an enhanced comprehension of the evolution of PAP families and the exploration of the genes of interest.

Aberrant DNA methylation of EDNRB, MGMT and TIMP3 gene promoters in saliva of head and neck carcinoma patients as a diagnostic tool.

Differential DNA methylation in the promoter region of tumour suppressor genes leads to gene function silencing. In this study, we aimed to evaluate the salivary promoter methylation of EDNRB, MGMT and TIMP3 genes in H&NC patients (n = 100), premalignant lesions patients (n = 25) and healthy controls (n = 50). Blood and saliva samples were collected from all three groups and 20 concomitant tumour tissues were collected from the H&NC patients. Probe-based Methylation-specific PCR (MSP) was performed to assess the relative quantification of methylation. Significant promoter hypermethylation was detected in all three genes between H&NC patients vs. healthy controls and premalignant lesion patients vs. healthy controls. Spearman correlation analysis showed, no significant association between methylation levels and clinicopathological characteristics of HNC patients while tobacco smoking was significantly related to EDNRB methylation in premalignant lesions. The receiver operating curve (ROC) generated for EDNRB, MGMT and TIMP3 genes from saliva samples was able to differentiate between cancer vs. healthy controls and premalignant vs. healthy controls. The combined diagnostic efficiency of the panel was higher than the genes singly. The combined sensitivity of EDNRB and TIMP3 increased to 92%. This indicates that EDNRB and TIMP3 have potential value in clinical practice as effective diagnostic markers for H&NC using saliva samples.

Genome-Wide Identification of the Kinesin Gene Family in Soybean and Its Response to Salt Stress

The kinesin (KIN) gene family is a subgroup of motor proteins. It plays a critical role in plant development and responses to environmental stresses. However, their function in soybean salt tolerance has yet to be clearly defined. This study employed bioinformatics approaches and identified 139 kinesin family members in the soybean genome. These 139 genes were classified into 10 subgroups, unevenly distributed across the chromosomes. The promoter regions of GmKIN genes harbored several stress-responsive elements, and segmental duplication was the primary driver of the expansion of the GmKIN gene family. Based on publicly available RNA-seq data, we studied the response patterns of 139 GmKIN genes to salt stress and found that 20 KIN genes in soybeans were upregulated after salt stress, with GmKIN114, GmKIN102, GmKIN109, and GmKIN99 showing more than a threefold increase in their expression under salt stress. Using quantitative fluorescence PCR, transgenic yeast, and a transgenic hairy root system, we preliminarily validated the salt tolerance functions of the four KIN genes in soybeans. This study probed into the GmKIN gene family in soybean, offering valuable insights into the functional roles of these genes in stress adaptation.

Genome-Wide Identification and Analysis of Carbohydrate-Binding Modules in Colletotrichum graminicola

Colletotrichum graminicola is the causative agent of both maize stem rot and leaf blight, which are among the most damaging diseases affecting maize. Carbohydrate-binding modules (CBMs) are protein domains that lack catalytic activity and are commonly found alongside carbohydrate-hydrolyzing enzymes in fungi. A comprehensive examination of the C. graminicola TZ-3 genome resulted in the identification of 83 C. graminicola CBM (CgCBM) genes, which are characterized by distinct gene structures and protein motifs. Subcellular localization analysis revealed that the majority of CgCBM proteins were localized in the extracellular space. Investigation of the promoter regions of CgCBM genes uncovered a variety of responsive elements associated with plant hormones, including abscisic acid and methyl jasmonate response elements, as well as various stress-related response elements for drought, cold, defense, and other stress factors. Gene ontology analysis identified the primary functions of CgCBM genes as being linked to polysaccharide metabolism processes. Furthermore, the 83 CgCBM genes exhibited varying responses at different time points during C. graminicola infection, indicating their contribution to the fungus–maize interaction and their potential roles in the fungal pathogenic process. This study provides essential insights into CgCBMs, establishing a crucial foundation for further exploration of their functions in the mechanisms of fungal pathogenicity.

Genome-wide identification and expression analysis of phytochrome gene family in Aikang58 wheat (Triticum aestivum L.).

Phytochromes are essential photoreceptors in plants that sense red and far-red light, playing a vital role in regulating plant growth and development through light signal transduction. Despite extensive research on phytochromes in model plants like Arabidopsis and rice, they have received relatively little attention in wheat. In this study, we employed bioinformatics methods to identify eight TaAkPHY genes in the Aikang58 wheat variety. Based on gene structure, conserved domains, and phylogenetic relationships, the TaAkPHY gene family exhibits a high degree of conservation. Synteny analysis revealed the evolutionary history of the PHY genes in Aikang58 and Chinese Spring wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), maize (Zea mays L.), quinoa (Chenopodium quinoa Willd.), soybean [Glycine max (L.) Merr.], and Arabidopsis [Arabidopsis thaliana (L.) Heynh.]. Among these species, wheat is most closely related to barley, followed by rice and maize. The cis-acting element analysis indicates that the promoter regions of TaAkPHY genes contain a large number of CAT-box, CGTCA-motif, GC-motif, etc., which are mainly involved in plant development, hormone response, and stress response. Gene expression profiling demonstrated that TaAkPHY genes exhibit varying expression levels across different tissues and are induced by various stress conditions and plant hormone treatments. Co-expression network analysis suggested that TaAkPHY genes may specifically regulate downstream genes associated with stress responses, chloroplast development, and circadian rhythms. Additionally, the least absolute shrinkage and selection operator (LASSO) regression algorithm in machine learning was used to screen transcription factors such as bHLH, WRKY, and MYB that influenced the expression of TaAkPHY genes. This method helps to quickly extract key influencing factors from a large amount of complex data. Overall, these findings provide new insights into the role of phytochromes in wheat growth, development, and stress responses, laying a foundation for future research on phytochromes in wheat.

A 6.49-Mb inversion associated with the purple embryo spot trait in potato

Abstract The embryo spot trait leads to a deep purple or reddish coloration at the base of the cotyledons of the embryo, visible on both sides of flat potato (Solanum tuberosum) seeds. This trait has long been used by potato researchers and breeders as a morphological marker during dihaploid induction. The formation of embryo spots reflects the accumulation of anthocyanins, but the genetic basis of this trait remains unclear. In this study, we mapped the embryo spot trait to a 6.78-Mb region at the end of chromosome 10 using an F2 population derived from a cross between spotted and spotless plants. The recombination rate in the candidate region is severely suppressed, posing challenges for the map-based cloning of the underlying gene and suggesting large-scale rearrangements in this region. A de novo genome assembly of the spotted individual and a comparative genomic analysis to the reference genome of spotless potato revealed a 6.49-Mb inversion present in the spotted plant genome. The left breakpoint of this inversion occurred in the promoter region of an R2R3 MYB transcription factor gene that is highly expressed in the cotyledon base of spotted embryos but is not expressed in that of spotless embryos. This study elucidated the genetic basis for embryo spot formation in potato and provides a foundation for future cloning of the causative gene.