Current Genetics最新文献

Trichoderma virens, a plant- beneficial fungus, has the ability to produce volatile and non-volatile secondary metabolites that possess antimicrobial properties and contribute to promoting plant growth and development. Gliovirin, viridin, viridiol, and heptelidic acid are among its major non-volatile metabolites. In our previous study, we observed that the deletion of heptelidic acid synthase (has1), a terpene cyclase, abolished the biosynthesis of major non-volatile metabolites, in addition to heptelidic acid. Conversely, deletion of the Tex7 gene, a non-ribosomal peptide synthetase, led to an increase in heptelidic acid production, along with other major secondary metabolites. Additionally, disruption of a GAPDH gene located within a secondary metabolite gene cluster abolished heptelidic acid biosynthesis and, consequently, all major secondary metabolites. These findings suggest that heptelidic acid might act as a microbial hormone that regulates secondary metabolism. To investigate this further, we conducted transcriptomic and metabolomic comparisons between the wild-type strain and a Δhas1 mutant lacking heptelidic acid biosynthesis. Transcriptome analysis revealed a major proportion of transcripts were down regulated. Of them, nine transcripts belonged to gliovirin biosynthesis cluster, 14 for viridin cluster and five for volatile sesquiterpene and heptelidic acid biosynthesis cluster; metabolite analysis couldn't detect any heptelidic acid along with viridin, viridiol and gliovirin in the Δhas1 mutant. Additionally, several other secondary metabolites were significantly down regulated. Our results are indicative of a possibility that heptelidic acid might function as a microbial hormone regulating secondary metabolism in this biotechnologically important fungus.

The genus Kluyvera has gained increasing attention due to their emerging role as opportunistic pathogens and their antibiotic resistance determinants. Various approaches have been employed to reveal genomic insights into the evolution and pathogenicity of Kluyvera species. However, detailed knowledge about Kluyvera-specific clustered regularly interspaced short palindromic repeats (CRISPR) is still missing. In this study, a genome-mining approach was employed for the characterization of CRISPR-Cas loci in a total of 13 complete Kluyvera genomes using CRISPRCasFinder and related tools. Out of 13 species, only K. ascorbata displayed multiple CRISPR-Cas arrays and a complete set of cas genes characteristics of a type I-E system. Spacer analysis revealed potential targets within phage and plasmid sequences, indicating historical exposure to mobile genetic elements. Furthermore, a phylogenetic tree constructed using the Cas3 protein sequence positioned K. ascorbata closely with other enteric bacteria, including Salmonella spp. and Citrobacter spp. This study provides the first detailed insight into the CRISPR-Cas architecture of K. ascorbata. Although there is no significant diversity of the CRISPR-Cas system identified in this species, it can emphasize a role as active immune defenses against invaders and offer a foundation for future functional and evolutionary investigations. Moreover, difficulties in identification of the genus Kluyvera can be overcome through the CRISPR-Cas system using next-generation diagnostics tools.

Fusarium species are pathogens affecting the broodstock of farm-raised Fannabin prawns, resulting in significant economic losses. However, the genomic characteristics and pathogenic mechanisms of these causative Fusarium strains remain incompletely understood. We isolated a novel Fusarium strain, designated 1-Jan, from diseased prawns and confirmed its pathogenicity through artificial infection experiments. Whole-genome sequencing was performed using both PacBio and Illumina platforms. The assembled genome is 51.8 Mb in size, consisting of 54 scaffolds with an N50 length of 1,974 kb. Gene prediction using AUGUSTUS identified 9,769 putative genes. Comparative genomic analysis revealed that strain 1-Jan is closely related to Fusarium solani JS-169 and Nectria haematococca. Candidate pathogenicity genes were identified through annotation against the PHI, FCPD, DFVF, and CAZy databases, yielding 1,101, 126, 479, and 497 hits, respectively. Within the 1-Jan genome, SNP mutations were identified in 737 potential pathogenicity genes, and 859 out of 4,255 single-copy genes were classified as potentially pathogenic. Additionally, 95 of the 967 genes unique to strain 1-Jan were predicted to be involved in pathogenicity. The genome sequence of the 1-Jan strain and the pathogenicity-related genes identified in this study provide valuable insights into the molecular basis of Fusarium-induced diseases in prawns and offer insights for improving the management of fungal infections in aquaculture.

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.

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.