INTERACTIONS BETWEEN CYANOBACTERIA AND HETEROTROPHS UNDER DIFFERENT TROPHIC CONDITIONS
ABSTRACT: Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing interspecies interactions is dependent, at least initially, on the availability of model systems with well-annotated genomes and tractable genetics. We employed controlled cultivation and next-generation sequencing technology to identify transcriptional responses of euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and a marine facultative aerobe Shewanella putrefaciens W3-18-1 to investigate the effect of C sources and C flux directions on the interactions between these organisms.
Project description:Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole cell acetate uptake rates (WAUR) and cell viability, and for gene expression changes using Affymetrix GeneChip technology and RT-PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multi-drug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant. Experiment Overall Design: Cells of P. aeruginosa were grown in steady-state nutrient-limiting conditions using a minimal medium with acetate as the sole carbon source. PCP was added as a continuous input, and the samples were taken at timepoints corresponding to approximately 0.5, 1, and 2 generation times. Reactors were run at least in triplicate, and samples from duplicate WT reactors and a single RpoS- reactor were used for the microarrays. Gene expression is reported as the average fold-change associated with gene expression of PCP-shocked cells compared with the pre-PCP timepoint (0 hours) for the WT.
Project description:The dataset is a total transcriptome. RNA samples were obtained from fermentation of the Xcc strain B100 in minimal media named XMD (Schatschneider et al., 2013) with 30 g/L glucose as a sole carbon source and 0.4 g/L KNO3 as the sole nitrogen source . the RNA probes were harvested in the middle of the growth phase at an OD = 1 and the library was prepared following the protcol published by Pfeifer-Sancar et al., 2013.
Project description:Desulfitobacterium hafniense DCB-2, a halo-respirer and versatile inorganic ion reducer, grows in hazardous waste contaminated environments. Gene expression changes were determined when the strain was grown in the presence of high concentrations of Fe(+3), Se(+6), U(+6), or NO3(-) as alternative electron acceptors. (Thesis by Christina L. Harzman at Michigan State University, 2009) RNA was used to directly compare gene expression in control samples of pyruvate fermentation (20 mM) to fermentation in the presence inorganic electron acceptors or respiration-inducing conditions. The inorganic electron acceptors added to media for fermentation were 1 mM selenate or 0.5 mM uranyl acetate. The respiration-inducing conditions were 50 mM ferric citrate (20 mM lactate carbon source) or 10 mM nitrate (20 mM lactate carbon source). Microarray hybridizations were performed with a dye swap and 3 biological replicates for a total of 6 slides per condition for comparison.
Project description:The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium) To explore the effect of various growth phases in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles growth in two sets media was compared to each other. Strain was grown in chemostat at 20% O2 in batch culture. Samples were collected in duplicate from both experiments.
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis or Methanospirillum hungatei in chemostats at a low growth rate of 0.027h-1. 7 samples of Desulfovibrio alaskensis strain G20 grown in syntrophic coculture on lactate with either Methanococcus maripaludis (4 replicates) or Methanospirillum hungatei (3 replicates), and 5 samples of sulfate-limited monoculture growth of strain G20 on lactate.
Project description:Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa has been shown to express and secrete plant cell wall associated enzymes. To better understand genes specifically associated with degradation of hemicellulose, we identified 353 genes by transcriptome analysis of N. crassa wild type strain grown on beechwood xylan. Exposure to xylan induces 9 of the 19 predicted hemicellulase genes. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of wild type showed that none were essential for growth on beechwood xylan. The transcription factor XlnR/Xyr1 in Aspergillus and Trichoderma species is considered to be the major transcriptional regulator of genes encoding both cellulases and hemicellulases. We identified a xlnR/xyr1 homolog in N. crassa, NCU06971, termed xlr-1 (xylanase regulator 1). Deletion of xlr-1 in N. crassa abolishes the growth on xylan and xylose, but growth on cellulose was indistinguishable from wild type. To determine regulatory mechanisms associated with hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose and xylanolytic versus cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. However, in N. crassa, xlr-1 is subject to non-CRE-1 mediated CCR. This systematic analysis provides the similarities and differences of hemicellulose degradation and regulation mechanisms used by N. crassa in comparison to other filamentous fungi. Four-condition experiments (minimal medium, xylan medium,xylose and Avicel medium) of mutant strain(xlr-1) compared to wild type strain; Cy3 and Cy5 dye swap
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis in chemostats at a high growth rate of 0.047h-1 5 replicates of coculture and 3 replicates of sulfate-limited monoculture
Project description:To understand how cell physiological state affects mRNA translation, we used the bacterium Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein–mRNA ratios were primarily due to differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Transcription levels were significantly altered for 26% of the protein changes; translational efficiency was significantly altered for 46% and a combination of both was responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part due to altered tRNA pools, is a major determinant of regulated alterations in protein expression levels in bacteria. For further details, see the resulting publication and its supplemental material: Taylor, R. C. et al., "Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria", Integrative Biology, 2013, 5, 1393. DOI: 10.1039/c3ib40120k mRNA profiles of Shewanella MR-1 were generated by sequencing on SOLID sequencers under high (20%) or low (8.5%) oxygen, with primary sample comparison pair in triplicate, other samples in duplicate.