Project description:endogenous small RNAs from Chlamydomonas reinhardtii strain J3(mt-) vegetative cells Keywords: High throughput 454 small RNA sequencing
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
Project description:Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.
Project description:The whole proteome analysis of the Pseudomonas sp. FIP_A4 strain in presence and absence of fipronil was conducted to evaluate the differentially expressed enzymes that can play role in fipronil degradation.
Project description:Bacterial antimicrobial compounds and global regulatory networks are typically studied as separate systems, limiting our understanding of how these functions might be integrated. Here we reveal a dual-function system in the biocontrol strain Pseudomonas sp. MUP55, where the pvf cluster simultaneously functions as a global regulator of specialized metabolism and produces direct antimicrobial compounds. Metabolomic and transcriptomic analysis of a ∆pvfC mutant showed extensive global change of the regulation of metabolites and gene expression, with effects on specialized metabolites. Remarkably, pvfC differentially regulates dual siderophore systems and uncouples typically co-regulated small regulatory RNAs in the Gac/Rsm cascade. Heterologous expression confirmed the pvf cluster produces compounds with direct antimicrobial activity independent of its regulatory functions. Comparative genomic analysis revealed the MUP55 pvf cluster contains a rare additional pvfE gene found in only 3.4% of identified pvf clusters. This evolutionary integration of regulatory and defensive functions within a single genetic system provides an efficient strategy for bacterial competitive fitness and resource allocation, expanding our understanding of how beneficial microbes coordinate cellular processes while maintaining environmental competitiveness
Project description:RNA-seq analysis of Pseudomonas sp OST1909 exposed to various preparations of naphthenic acids samples led to the identiifcation of many NA-induced genes.
