Project description:We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
Project description:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post infection with Xanthomonas oryzae pv. oryzae strain PXO99 , the goal is to understand the transcriptomic response of rice roots to colonization by bacterial pathogen
Project description:In this study, we isolated a potent doxycycline-degrading bacterium, Chryseobacterium sp. WX1, from environmental samples. To elucidate the molecular mechanisms underlying doxycycline degradation by strain WX1, we assessed and interpreted the proteomic profiles of Chryseobacterium sp. WX1 under conditions both with and without doxycycline exposure.
Project description:Transcription profiling of the DSF regulon in Xanthomonas oryzae pv. oryzae (Xoo) using wild type and the rpfF mutant. Cell-cell signaling mediated by the quorum sensing molecule known as Diffusible Signaling factor (DSF) is required for virulence of Xanthomonas group of plant pathogens. DSF in different Xanthomonas and the closely related plant pathogen Xylella fastidiosa regulates diverse traits in a strain specific manner. The transcriptional profiling performed in this study is to elucidate the traits regulated by DSF from the Indian isolate of Xanthomonas oryzae pv. oryzae, which exhibits traits very different from other Xanthomonas group of plant pathogen. In this study, transcription analysis was done between a wild type Xanthomonas oryzae pv. oryzae strain and an isogenic strain that has a mutation in the DSF biosynthetic gene rpfF.
Project description:African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. The genes whose induction is of benefit to the pathogen are called susceptibility genes. RNA profiling experiments in rice using the Malian Xoo strain MAI1 and in silico prediction of TAL effector binding sites were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor.
Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.
Project description:Purpose: The purpose of this experiment is to expand the repertoire of C. elegans edited transcripts and identify the roles of ADR-1 as indirect regulator of editing and ADR-2 as the only active deaminase in vivo. Methods: Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline. Results: Despite lacking deaminase function, ADR-1 affects editing of over 60 adenosines within the 3’ UTRs of 16 different mRNAs. Furthermore, ADR-1 interacts directly with ADR-2 substrates, even in the absence of ADR-2; and mutations within its dsRNA binding domains abolished both binding and editing regulation. Conclusions: ADR-1 acts as a major regulator of editing by binding ADR-2 substrates in vivo and raises the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing by deaminase-independent mechanisms. Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline.
Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources
Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease. Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.
