Current Genetics最新文献

Trichoderma species exhibit remarkable versatility in adaptability and in occupying habitats with lifestyles ranging from mycoparasitism and saprotrophy to endophytism. In this study, we present the first high-quality whole-genome assembly and annotation of T. lixii using Illumina HiSeq technology to explore the mechanisms of endophytic lifestyle and plant colonization. The genome size was 41.1 Mbp, comprising 15,430 predicted genes, of which 7,918 were functionally annotated. Comparative analysis identified 82 CAZyme families involved in cellulose and hemicellulose degradation, notably Glycoside Hydrolases (GHs) (43) [e.g., GH3 (14), GH5 (10), GH7 (4) ], Carbohydrate Esterases (CEs) (10), and Auxiliary Activities (AAs) (29) [e.g., AA3 (20), AA9 ]. GHs primarily degrade cellulose, while Polysaccharide Lyases (PLs), along with other CAZymes like CEs and Lytic Polysaccharide Monooxygenases (LPMOs), assist in modifying substrates or targeting specific bonds. These enzymes facilitate substrate breakdown, host tissue penetration, and nutrient acquisition, supporting a non-pathogenic, endophytic lifestyle. The presence of 53 secondary metabolite biosynthetic gene clusters indicates a strong biosynthetic potential. KEGG analysis assigned 2,469 genes to multiple metabolic and signaling pathways, highlighting an enriched profile for carbohydrate metabolism, signal transduction, and antibiotic biosynthesis. Comparative genomics also revealed both preserved and distinctive traits of T. lixii, confirming its ecological flexibility and promise as a source of new bioactive molecules. These findings reveal genetic diversity among the species, providing a foundation for future studies on biocontrol and endophytic functions. The growing availability of Trichoderma genomes deepens understanding of their unique features and offers new prospects for agricultural and biotechnological applications.

Telomerase plays an important role in sustaining eukaryotic linear chromosomes, as elongation of telomeres is needed to counterbalance the shortening occurring in each replication round. Nevertheless, in telomerase-deficient cells, Alternative Lengthening of Telomeres (ALT) pathways can maintain telomeres by employing recombination-based mechanisms. In the budding yeast Naumovozyma castellii, effective activation of the ALT pathway leads to bypass of senescence and supports long-term growth. We found that telomere structures in N. castellii ALT cells are stably maintained at a shortened uniform length over extensive numbers of generations. This is correlated to the spreading of a subtelomeric sequence, TelKO element, to all telomeres. Genome sequencing of the wild-type strain revealed variants of the TelKO element, differing in their lengths, and separate ALT strains are maintained by spreading of distinct TelKO element variants. Although short uniform telomere structures are predominant, sporadic telomere lengthening events occur by addition of long repeated arrays of TelKO elements. The telomere-binding protein Rap1 can bind to TelKO sequences in vitro, indicating a functional role of TelKO elements in providing stability to shortened ALT telomeres. Our results suggest that stable maintenance and telomere functionality may be achieved by incorporating the distal subtelomeric TelKO sequences into the telomeric chromatin cap.

Advances in diagnostics, therapeutics, and large-scale clinical studies have significantly expanded our understanding how human health is shaped by the microorganisms that colonize the body since birth. This article explores the rapidly evolving field of human microbiome research, focusing upon how microbial communities influence neurological health and contribute to the development of neurodegenerative diseases (NDs). Multiple factors, including age, lifestyle, and immunological memory, are recognized as major determinants of an individual's microbiome composition, which in turn can influence the onset and the progression of disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. These conditions have been linked to mechanisms including the aggregation of pathogenic proteins (e.g., amyloid-β and α-synuclein), inflammation driven by activation of the Toll-like receptor (TLR) signaling pathway, the NLRP3 inflammasome, as well as the modulatory effect of microbial metabolites such as short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS). The article also highlights ongoing research and emerging strategies aimed at leveraging the human microbiome for better diagnosis, and management of NDs.

Clearance and adaptation to reactive oxygen species (ROS) are crucial for cell survival. As in other eukaryotes, the catalases in Neurospora crassa are the main enzymes responsible for ROS clearance, primarily by decomposing hydrogen peroxide (H₂O₂), a major type of ROS. Their expression is tightly regulated by growth and environmental conditions. Histone modifications are frequently linked to the regulation of gene transcription. Histone H3 trimethylation at lysine 4 (H3K4me3) is one of the most studied histone modifications and is associated with transcription initiation. We showed that the abolishment of H3K4me3 in N. crassa led to a low CAT-3 expression level and increased sensitivity to H₂O₂-induced ROS stress. On the other hand, overexpression of the histone methyltransferase SET-1 led to increased expression of CAT-3. Furthermore, ChIP assays revealed that SET-1 mediated H3K4me3 modification at the cat-3 TSS and ORF 5' region, which regulates RNAPII recruitment for cat-3 transcription. Together, these results demonstrate that histone methyltransferase COMPASS (complex of proteins associated with Set1) complex-mediated H3K4me3 plays a key role in activating cat-3 expression in N. crassa.

Cadmium, a significant environmental heavy metal contaminant, poses considerable threats to human health. Cadmium detoxification by microbes, especially yeast, would serve as a potential strategy for coping with cadmium contamination. Based on the screening assay, the non-conventional yeast Wickerhamomyces anomalus BT3 exhibits cadmium stress resistance with a MIC of CdCl₂ exceeding 1000 µM. A prolonged lag phase was observed when BT3 was exposed to > 400 µM cadmium prior to resuming growth in log phase. Thus, suggesting the presence of a cadmium-tolerant genotype in BT3 genomes. Based on the whole genome sequencing analysis, BT3 has a genome size of ~ 14Mbp with 35.0% GC content. Functional gene annotation against the EggNOG and KEGG databases revealed that most of the genes are involved in the genetic translation process. Several key genes potentially involved in cadmium tolerance were identified, including the Yeast cadmium factor (YCF1) gene, which encodes a transporter protein important for cellular homeostasis and detoxification. Genes involved in glutathione synthesis (GSH2) were detected to support the activity. In addition, genes related to oxidative stress response pathways, such as SOD1/2, TRX1, GLRX, and PRX1, were present in BT3 genomes, which promote survival under cadmium-induced oxidative stress conditions. Comparative genome analysis revealed that 2212 gene clusters (36% of BT3 gene clusters) were shared between yeasts. Interestingly, 121 gene clusters were found to be unique to BT3, which predominantly correlated with the gene ontology terms of transmembrane transport activity, integral membrane component, and dimethyl sulfide monooxygenase for the sulfur cycle. Further studies are required to clarify the potential involvement of these unique genetic properties of BT3 in coping with cadmium exposure.

With the day to day increase in energy consumption due to increase in urbanization production of bioethanol is highly in demand. At this point where the traditional methods are not able to suffice the demands due to its high cost and low productivity, new methods need to be developed. This review aims to understand the importance and the regulation of ADH2 in Saccharomyces cerevisiae because Adh2p is the only enzyme that initiates the reaction for the conversion of ethanol, the end product of fermentation to acetaldehyde. The effect of glucose on regulatory mechanisms of Alcohol dehydrogenase II (ADH2) with respect to Snf1 kinase, Target of Rapamycin (TOR) and CCR4 (Carbon Catabolite Repression) pathway on S. cerevisiae are discussed. Snf1 is a serine threonine kinase which is inactive in presence of high glucose concentrations and gets activated in low glucose environments which in turn affects the transcription of ADH2 by controlling the upstream TFs (Transcription Factors). TOR pathway is an essential signalling network that senses the availability of nutrients, mostly glucose and amino acids. This gets activated in presence of glucose. TORC1 regulates the transcription of ADH2 via various downstream transcription factors like Sch9p, Rim15, etc. Another global transcription factor CCR4, regulates ADH2 by acting directly upon its promoter region. The unique function of Adh2p in yeast metabolism, has directed numerous research work making it a vital target. Genetic manipulation of ADH2 gene has proved to be beneficial for food, bioethanol industry.

This study records, revalidates and describes Ballistura fitchioides Denis 1947 from the Nilgiris, Western Ghats, India. This species is part of the B. fitchi species group, distinguished by a reduced number of chaetae on the anterior and posterior sides of the dens. The study also reports a 13,492-bp-long mitochondrial genome, which contains 33 genes, including 12 protein-coding genes and the remaining 19 tRNA and two rRNA genes. The complete mitogenome data of B. fitchioides serves as a draft genome for understanding the genetic relationships among species in the genera.

Non-typhoid Salmonella are among the main causes of foodborne diseases worldwide. However, information on rare serovars is scarce, limiting the understanding of their prevalence, distribution and pathogenesis. Salmonella enterica serovar Inganda (S. Inganda) is a rare non-typhoid serovar. Considering the few existing reports, and the current use of genomics, this study characterized for the first time the antimicrobial resistance, pathogenic potential and diversity of S. Inganda genomes worldwide. A S. Inganda strain from human feces in 2018 in Brazil (SI264) had its resistance determined against 18 antimicrobials by disk-diffusion and had its genome sequenced. S. Inganda publicly available genomes (n = 12) were analyzed for genotypic resistance, stress and virulence genes, plasmids, pathogenicity islands, prophages, Multi-Locus Sequence Typing (MLST), core-genome MLST (cgMLST), and single-nucleotide polymorphisms (SNPs). SI264 showed no phenotypic resistance. All 12 S. Inganda genomes harbored genes or mutations for aminoglycoside (aac(6')-Iaa), quinolone (parC Thr57→Ser), and acid (asr) resistance, multi-drug efflux systems (mdsAB), and gold tolerance (golST). One genome from US harbored pKPC-CAV1321 plasmid. Nine pathogenicity islands, 174 Salmonella virulence genes, and 17 prophages were found in different frequencies. Although a great genomic diversity was noticed, S. Inganda genomes from US and UK were closely related. In conclusion, genomic analyses were able to characterize the current available genomes of S. Inganda strains mostly as genetically diverse, susceptible to antimicrobials, and potentially acid and heavy metal resistant. The presence of numerous virulence features also suggested their pathogenic potential, especially among clinical strains, and reinforced the importance to better characterize rare non-typhoid serovars.

Salmonella enterica subspecies enterica serovar Typhimurium, is a leading cause of gastroenteritis food-borne illness that leads to hospitalizations worldwide. These infections are further complicated because of the rapid development of antibiotic resistance and the spread of infections by the resistant strains. Thus, the overall aim of this study is to identify a multidrug-resistant strain of Salmonella Typhimurium, whole genome sequencing, and computational analysis of genome sequence. This study presents a comprehensive analysis of Salmonella Typhimurium ms203, isolated from a gastroenteritis patient in Odisha, India. The strain was characterized by microbiological and biochemical assays using a set of standard tests. An antibiotic-susceptibility test of the strain was carried out using VITEK system. Whole genome sequencing facilitated an in-depth examination of genomic architecture, distribution of pathogenic island regions, and antibiotic-resistant sequences. Utilizing diverse computational tools and bioinformatics analysis, including Prokka annotations, protein-protein interaction analysis, genomic island identification, plasmid and phage characterization, antibiotic resistance gene profiling, and average nucleotide identity (AAI) determination, this study elucidates key insights into the genetic makeup and pathogenic potential of S. Typhimurium ms203. These findings may provide valuable contributions to understanding the epidemiology, pathogenesis, and antibiotic resistance mechanisms of this Salmonella strain, with implications for public health interventions and surveillance strategies.

The DNA Damage Tolerance pathway (DDT) is one of the major mechanisms for resolving replication fork blocks. A key factor in DDT is the fork-associated clamp PCNA, which can undergo to mono- or polyubiquitination, leading to error-prone or error-free modes of DNA damage bypass, respectively. In the yeast Saccharomyces cerevisiae, Rad5^HLTF/SNF2 factor plays important roles in both pathways: (i) promoting the error-free mode through PCNA polyubiquitination and transient template switching and (ii) interacting with specialized DNA polymerases involved in the error-prone pathway. Rad5 also associates with telomeres, the repetitive DNA regions present at the ends of chromosomes. Telomeric DNA, tightly bound by tandem proteins arrays, poses unique challenges to replication fork progression. Here, I review the current understanding of the link between Rad5 and telomeres and provide evidence that Rad5 binds to yeast telomeres, with notable enrichment during telomere replication. This finding highlights a connection between telomeres and an important DDT factor in unperturbed wild-type cells, raising intriguing possibilities regarding the functional interplay between telomere replication and DNA damage tolerance mechanisms.