Current Genetics最新文献

{"title":"Antimicrobial resistance profiles and genomic insights of phenotypically extended spectrum β-lactamase-positive Klebsiella pneumoniae from cattle farms.","authors":"Neha Parmar, Randhir Singh, Anuj Tyagi, Simranpreet Kaur","doi":"10.1007/s00294-025-01326-9","DOIUrl":"https://doi.org/10.1007/s00294-025-01326-9","url":null,"abstract":"<p><p>Klebsiella pneumoniae, identified by the World Health Organization (WHO) as a critical priority pathogen, presents a growing public health concern due to increasing multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing strains. This study assessed the antimicrobial resistance (AMR) profiles of K. pneumoniae isolates from 288 cattle farm samples in Punjab, India. The bacterium was detected in 10.06% (29/288) of the samples, with 65.51% (19/29) of the isolates being MDR and 6.89% (2/29) exhibiting an ESBL-like phenotype. Resistance genes for β-lactams (bla_TEM-62.06%, bla_AmpC-51.72%, bla_SHV-51.72%), quinolones (qnrS-13.79%), and tetracyclines (tetA-10.34%) were identified. Whole-genome sequencing (WGS) was conducted on two representative phenotypically ESBL-positive and MDR K. pneumoniae isolates, selected for detailed genomic analysis within the limitations of available funding. The analysis revealed the presence of multiple antimicrobial resistance genes (ARGs) conferring resistance to quinolones, cephalosporins, carbapenems, tetracyclines, macrolides, and several other antibiotic classes. Virulence factors detected included Type I and Type III fimbriae, capsules, efflux systems, siderophores, and secretion systems. Plasmid replicon types (IncFIB(K), IncFIB, IncFII(K)), integrons harboring ARGs, and insertion sequences (ISKpn24, ISKpn1, ISKpn19, IS26) were also identified. Multilocus Sequence Typing (MLST) assigned isolates to sequence types ST-160 and ST-4232, with core-genome MLST identifying additional types ST-14,733 and ST-13,365. These findings highlight the potential risk of transmission of resistant K. pneumoniae strains between animals and humans and underscore the urgent need for integrated One Health surveillance and intervention strategies to contain the spread of AMR across sectors.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"23"},"PeriodicalIF":1.6,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyphasic characterization and genomic insights of the cyanobacteria Aphanothece microscopica and A. stagnina from Southern Brazil with emphasis on fatty acid biosynthesis.","authors":"Ronald Tarazona Delgado, Burkhard Becker, Ekaterina Pushkareva, Mathias Schäfer, Carlos Rafael Borges Mendes","doi":"10.1007/s00294-025-01328-7","DOIUrl":"https://doi.org/10.1007/s00294-025-01328-7","url":null,"abstract":"<p><p>Cyanobacteria are ecologically pivotal microorganisms with immense biotechnological potential, particularly due to their capacity to synthesize fatty acids, terpenes, and other metabolites with applications ranging from biofuels to nutraceuticals. Despite this, many genera remain genomically underexplored. In this study, we present a polyphasic genomic analysis of two native strains, Aphanothece microscopica RSMan92 and A. stagnina RSMan2012, isolated from the Patos Lagoon estuary in Southern Brazil. Whole-genome sequencing and annotation enabled characterization of both genomes: RSMan92 spans 3.69 Mb in 701 contigs with 3,279 protein-coding sequences, while RSMan2012 comprises 3.28 Mb in 153 contigs with 3,567 protein-coding sequences. Phylogenetic analyses using MUSCLE and RAxML positioned these strains within a well-supported clade closely related to other Aphanothece RefSeq genome, highlighting their evolutionary relatedness and reinforcing the integrative taxonomic placement of the genus. Both strains reveal conserved gene repertoires associated with stress response, fatty acid biosynthesis, and secondary metabolite production (terpenes). Functional classification based on COG and KEGG annotations indicated strong representation of genes involved in lipid metabolism. To investigate how variations in temperature and light intensity modulate metabolite profiles, cultures were subjected to different environmental conditions. GC/EI-MS analysis revealed distinct patterns of fatty acid methyl ester production across conditions: both strains synthesized saturated and monounsaturated fatty acids, whereas only strain RSMan92 exhibited the capacity to synthesize polyunsaturated fatty acids, including linoleic acid derivatives, under variable cultivation conditions. This polyphasic genomic approach, providing novel genomic records, also reveals the fatty acid biosynthetic capacity and metabolic plasticity of Aphanothece strains, emphasizing their biotechnological relevance.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"22"},"PeriodicalIF":1.6,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of intraperitoneal cannabidiol (CBD) injection on intestine microbiome profile in a mouse model.","authors":"Igor Jasielczuk, Ewa Ocłoń, Jakub Żurowski, Tomasz Szmatoła, Karolina Mizera-Szpilka, Artur Gurgul","doi":"10.1007/s00294-025-01327-8","DOIUrl":"10.1007/s00294-025-01327-8","url":null,"abstract":"","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"21"},"PeriodicalIF":1.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12484330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome assembly and comparative genomic analyses provide insight into the endophytic lifestyle of Trichoderma lixii.","authors":"Arjan Singh, Meenu Katoch","doi":"10.1007/s00294-025-01324-x","DOIUrl":"https://doi.org/10.1007/s00294-025-01324-x","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"20"},"PeriodicalIF":1.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtelomeric elements provide stability to short telomeres in telomerase-negative cells of the budding yeast Naumovozyma castellii.","authors":"Rishi K Jaiswal, Teresa Garibo Domingo, Héloïse Grunchec, Komudi Singh, Mehdi Pirooznia, Eran Elhaik, Marita Cohn","doi":"10.1007/s00294-025-01325-w","DOIUrl":"10.1007/s00294-025-01325-w","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"19"},"PeriodicalIF":1.6,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12408736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144945874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of the human microbiome in neurodegenerative diseases: A Perspective.","authors":"Nilabha Mukherjea, Ashwin Khandelwal, Rohit Saluja, Neetu Kalra","doi":"10.1007/s00294-025-01319-8","DOIUrl":"https://doi.org/10.1007/s00294-025-01319-8","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"17"},"PeriodicalIF":1.6,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144946012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SET-1-mediated H3K4me3 modification regulates catalase-3 expression in Neurospora crassa.","authors":"Yupeng Zhao, Qun He, Muqun Yu","doi":"10.1007/s00294-025-01320-1","DOIUrl":"https://doi.org/10.1007/s00294-025-01320-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"18"},"PeriodicalIF":1.6,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144946076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tolerance of the non-conventional yeast Wickerhamomyces anomalus BT3 to cadmium exposure: a genomic characterization.","authors":"Nadhila Mutia Afsari, Sri Listiyowati, Indra Maulana, Rika Indri Astuti","doi":"10.1007/s00294-025-01322-z","DOIUrl":"10.1007/s00294-025-01322-z","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"16"},"PeriodicalIF":1.6,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Possible regulatory network and associated pathways governing the expression of ADH2 in Saccharomyces cerevisiae.","authors":"Pratima Sarkar, Rohan Nath, Prity Adhikary, Arindam Bhattacharjee","doi":"10.1007/s00294-025-01321-0","DOIUrl":"10.1007/s00294-025-01321-0","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"15"},"PeriodicalIF":1.6,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Description of Ballistura fitchioides (Collembola; Isotomidae) from the Wayanad, Kerala, India with its mitogenome.","authors":"Jose Anjooriya, Javier Ignacio Arbea, Senthilkumar Narmatha, Guru Pada Mandal, Raveendranathanpillai Sanil","doi":"10.1007/s00294-025-01316-x","DOIUrl":"https://doi.org/10.1007/s00294-025-01316-x","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"14"},"PeriodicalIF":1.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}