Sordaria fimicola, a coprophilous ascomycete, is a homothallic fungus that can undergo sexual differentiation with cellular and morphological changes followed by multicellular tissue development to complete its sexual cycle. In this study, we identified and characterized the blue-light photoreceptor gene in S. fimicola. The S. fimicola white collar-1 photoreceptor (SfWC-1) contains light-oxygen-voltage-sensing (LOV), Per-Arnt-Sim (PAS), and other conserved domains and is homologous to the WC-1 blue-light photoreceptor of Neurospora crassa. The LOV domain of Sfwc-1 was deleted by homologous recombination using Agrobacterium-mediated protoplast transformation. The Sfwc-1(Δlov) mutant showed normal vegetative growth but produced less carotenoid pigment under illumination. The mutant showed delayed and less-pronounced fruiting-body formation, was defective in phototropism of the perithecial beaks, and lacked the fruiting-body zonation pattern compared with the wild type under the illumination condition. Gene expression analyses supported the light-induced functions of the Sfwc-1 gene in the physiology and developmental process of perithecial formation in S. fimicola. Moreover, green fluorescent protein (GFP)-tagged SfWC-1 fluorescence signals were transiently strong upon light induction and prominently located inside the nuclei of living hyphae. Our studies focused on the putative blue-light photoreceptor in a model ascomycete and contribute to a better understanding of the photoregulatory functions and networks mediated by the evolutionarily conserved blue-light photoreceptors across diverse fungal phyla. IMPORTANCE Sordaria sp. has been a model for study of fruiting-body differentiation in fungi. Several environmental factors, including light, affect cellular and morphological changes during multicellular tissue development. Here, we created a light-oxygen-voltage-sensing (LOV) domain-deleted Sfwc-1 mutant to study blue-light photoresponses in Sordaria fimicola. Phototropism and rhythmic zonation of perithecia were defective in the Sfwc-1(Δlov) mutant. Moreover, fruiting-body development in the mutant was reduced and also significantly delayed. Gene expression analysis and subcellular localization study further revealed the light-induced differential gene expression and cellular responses upon light stimulation in S. fimicola.
Background: During the past few years, Klebsiella pneumonia has become a threat to human health because emerging strains could be both multidrug resistant and hypervirulent. In this project, we explored the regulatory mechanisms underlying the drug resistance of a carbapenem-resistant hypervirulent (CR-hv) Klebsiella pneumoniae strain. The specific aims are as follows: 1) generating a complete reference genome; 2) finding differentially expressed genes and operons; 3) finding differentially expressed antisense transcripts and sRNAs implicated in stress response. Materials and Methods: The whole genome sequencing of a CR-hv KP isolate, TVGHCRE225, was performed by using RSII system, Pacific Bioscience of California, Inc. To investigate the transcriptome changes of TVGHCRE225 under the treatments of antibiotics, this KP strain was cultured in separated media containing colistin and tigecycline, respectively. Then eight samples collected at the mid-log and log phases were taken to perform RNA-seq and sRNA-seq experiments for transcriptome profiling. Additionally, using bioinformatics approaches we predicted and annotated sRNAs in all the non-protein coding regions, including the antisense strand of known protein-coding genes. Results: The assembled genome for TVGHCRE225 consists of the 5.5-Mbp chromosome and three plasmids. 5,895 genes were predicted and 65 of them were hypothetical. One plasmid is pLVPK-like, which harbors capsular-gene transcription factors, rmpA and rmpA2, and a ferric aerobactin receptor, iutA, providing an explanation to the high virulence of this KP isolate. Additionally, ~300 novel non-coding RNA genes and ~50 antisense transcripts were identified from the RNAseq and sRNA-seq results. Noticeably, under the treatments of two different antibiotics, respectively, distinct sets of differentially expressed genes (DEGs) were identified, with only a few genes co-occurred. Changes over the operon structures with varied member genes were observed and such structural changes could be categorized into merged/extended, shortened, and mixed types. Conclusions: Those DEGs along with the structurally changed operons under antibiotics treatment were implicated in a diverse range of biological pathways, not just the well-known stress responses. Our findings suggest that antibiotics resistance of bacteria might be highly regulated where a number of noncoding RNAs such as antisense transcripts and small RNAs may play critical roles.
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