Project description:<p>We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, <em>Paraburkholderia</em> sp. strain 1N. The growth of <em>Paraburkholderia</em> sp. 1N was monitored under aerobic conditions in a soil-extracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as <em>Paraburkholderia</em> sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of <em>Paraburkholderia</em> sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression.</p><p><strong>IMPORTANCE:</strong> Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here, we show that growth of a bacterial soil isolate, <em>Paraburkholderia</em> sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content are used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with <em>Paraburkholderia</em> sp. 1N, which belongs to a metabolically diverse genus, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.</p>
Project description:Isolation and characterization of two recently isolated Novosphingobium oxfordensis sp. nov. and Novosphingobium mississippiensis sp. nov. strains from soil, with LCMS and genome-based investigation of their glycosphingolipid productions
Project description:We found that a novel gene BC094916 mRNA significantly decreased in plasma cells. Because of plasmablast-like, mus musculus myeloma SP 2/0 cell line was selected to test the effect of BC094916 overexpression on plasmablast/plasma cells. BC094916 cDNA (General Biosystems, Anhui, China) was cloned into lentiviral vector LV122 or LV201 (Fugene Corp., Guangzhou, China) to generate BC094916 and BC094916-EGFP fusion protein, respectively. BC094916-expressing LV122 was then transfected into SP 2/0 cells, and stable transfectants were identified by drug selection (Puromycin, Sigma, 10 μg/ml). BC094916 overexpression suppressed SP 2/0 cell proliferation by inducing cell apoptosis. Importantly, BC094916 overexpression effectively suppressed tumor progression in the SP 2/0 xenograft mouse model. In addition, we found that BC094916 is a suppressive transcriptional factor. To verify its target genes, we determined mRNA profiles in BC094916-overexpressed and vector-transduced SP 2/0 cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.
