Complete Genome Sequencing and Transcriptome Analysis of aniline-degrading strain T1
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ABSTRACT: The aniline-degrading strain T1 can efficiently degrade aniline, however, it is not clear which key genes are associated with aniline degradation, and we have adopted a genome-wide and transcriptomic approach to fully understand the microbial degradation mechanism of aniline.
Project description:The NGS-aided mRNA-seq analysis was conducted to survey transcriptome changes by each of following mutations; bz1728, bz1728nobiro6, nbr6-t1 or taf12-t1.
Project description:Insulin degrading enzyme (IDE) is a major enzyme responsible for insulin degradation in the liver. The modulation of insulin degrading enzyme activity is hypothesized to be a link between T2DM and liver cancer. Results provide insight into role of IDE in proliferation and other cell functions.
Project description:The biodegradation of lignite (brown coal) by microorganisms has the potential for bioremediation of contaminated mining sites and to generate alternative ways to valorize lignite, such as by producing humic acids or building block chemicals. Previously, a lignite-degrading strain of Trichoderma was isolated, but the genomic and transcriptomic basis of its lignite-degrading ability remained unknown. Here we report that the sequenced genome of the T. cf. simile WF8 strain encoded for enzymes with roles in the degradation of lignite, and potentially tolerance to lignite-breakdown products. There was only a small number of annotated unique genes in the T. cf. simile WF8 genome compared to other fungi, and likely the expression of gene families shared with other fungi is a key factor in lignite biosolubilization by T. cf. simile. The transcriptomes were analyzed of T. cf. simile cultured at two time-points with the lignite-breakdown model compounds 4-phenoxybenzoic acid (which was growth inhibitory), and phenetole and 9-10-dibutoxyanthracene (neither of which inhibited growth), and showed ~20% of genes up-regulated by one or more of these compounds. The analysis highlights candidates for characterization and engineering enzyme over-expressing T. cf. simile strains with potentially improved degradation capacity, e.g., laccases and peroxidases, or tolerance and catabolism of breakdown products, e.g., cytochrome P450s, and ring cleavage dioxygenases. Published in International Biodeterioration & Biodegradation (https://doi.org/10.1016/j.ibiod.2025.105997)
Project description:Insulin degrading enzyme (IDE) is a major enzyme responsible for insulin degradation in the liver. The modulation of insulin degrading enzyme activity is hypothesized to be a link between T2DM and liver cancer. Results provide insight into role of IDE in proliferation and other cell functions. HepG2 cells were transfected with 96nM siRNA for IDE or AllStars Negative Control siRNA (Qiagen) using Lipofectamine 2000 (Invitrogen). 16 h after transfection, cells were treated with 10 nM insulin (Sigma Aldrich) or vehicle for 24 h in serum starvation condition. Total RNA was extracted. For each of the 4 conditions, 3 biological replicates were included.
Project description:Stage T1 bladder cancers have the highest progression and recurrence rates of all non-muscle invasive bladder tumors. T1 tumors are heterogeneous; while most T1 patients are treated with BCG, many will progress and die from bladder cancer, and particularly aggressive tumors could be treated by early cystectomy. To better understand the molecular heterogeneity of T1 cancers, we performed transcriptome profiling and unsupervised clustering, identifying five consensus subtypes of T1 tumors treated with reTUR, induction and maintenance BCG. The T1-LumGU subtype was associated with CIS (6/13, 46% of all CIS), had high E2F1 and EZH2 expression, and enriched E2F target and G2M checkpoint Hallmarks. T1-Inflam was inflamed and infiltrated with immune cells. While most T1 tumors were classified as luminal papillary, the T1-TLum subtype had the highest median Luminal Papillary score and FGFR3 expression, no recurrence events, and the fewest copy number gains. T1-Myc and T1-Early subtypes had the most recurrences (14/30 within 24 months), highest median MYC expression, and, when combined, had significantly worse recurrence-free survival than the other three subtypes. T1-Early had 5 (38%) recurrences within the first 6 months of BCG, and repressed IFN-alpha and IFN-gamma Hallmarks and inflammation. We developed a single-patient T1 classifier and validated our subtype biology in a second cohort of T1 tumors. Future research will be necessary to validate the proposed T1 subtypes and to determine if therapies can be individualized for each subtype.