The biosynthetic gene cluster for chlorothricin (CHL) was localized to a 122 kb contiguous DNA from Streptomyces antibioticus DSM 40725, and its involvement in CHL biosynthesis was confirmed by gene inactivation and complementation. Bioinformatic analysis of the sequenced 111.989 kb DNA region revealed 42 open reading frames, 35 of which were defined to constitute the CHL gene cluster. An assembly model for CHL biosynthesis from D-olivose, 2-methoxy-5-chloro-6-methylsalicyclic acid, and chlorothricolide building blocks was proposed. This work represents cloning of a gene cluster for spirotetronate antibiotic biosynthesis and sets the stage to investigate the unusual macrolide biosynthesis including tandem Diels-Alder cyclizations, Baeyer-Villiger oxidation, and incorporation of an enoylpyruvate unit.
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http://dx.doi.org/10.1016/j.chembiol.2006.03.008 | DOI Listing |
Front Plant Sci
January 2025
Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding, Haikou, China.
Introduction: Sweet potato is an important food, feed and industrial raw material, and its tubers are rich in starch, carotenoids and anthocyanins.
Methods: To elucidate the gene expression regulation and metabolic characteristics during the development of sweet potato tubers, transcriptomic and metabolomic analyses were performed on the tubers of three different sweet potato varieties at three developmental stages (70, 100, and 130 days (d)).
Results: RNA-seq analysis revealed that 16,303 differentially expressed genes (DEGs) were divided into 12 clusters according to their expression patterns, and the pathways of each cluster were annotated.
Synth Syst Biotechnol
June 2025
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
Genome mining has revealed that spp. possess numerous down-regulated or cryptic biosynthetic gene clusters (BGCs). This finding hinted that our investigation of fungal secondary metabolomes is limited.
View Article and Find Full Text PDFFront Genet
January 2025
Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, United States.
Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a , enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data.
View Article and Find Full Text PDFFront Immunol
January 2025
Department of Radiation Oncology, Lianyungang Second People's Hospital (Lianyungang Tumur Hospital), Lianyungang, China.
Background: Hepatocellular carcinoma (LIHC) poses a significant health challenge worldwide, primarily due to late-stage diagnosis and the limited effectiveness of current therapies. Cancer stem cells are known to play a role in tumor development, metastasis, and resistance to treatment. A thorough understanding of genes associated with stem cells is crucial for improving the diagnostic precision of LIHC and for the advancement of effective immunotherapy approaches.
View Article and Find Full Text PDFVirus Evol
January 2025
MRC-University of Glasgow Centre for Virus Research, The University of Glasgow, Glasgow G61 1QH, United Kingdom.
Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: , and , while we also present new genomes of the under-sampled , and genera.
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