Project description:In this study, expression analysis using electrochemically synthesized Combimatrix 12K DNA microarrays was validated in G sulfurreducens. Growth under nitrogen fixing conditions and growth in ammonium amended medium, respectively, were the experimental and control conditions. Expression analysis using this platform was also compared to expression analysis on whole cDNA microarrays. Keywords: two-condition comparison
Project description:Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Most frequently, antisense transcription is due to the overlap of mRNAs with long 5’ regions or 3’ ends that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO2-fixing cells and the nitrogen-fixing heterocysts. Differentiation of heterocysts depends on the global nitrogen regulator NtcA and requires the specific regulator HetR. To identify antisense RNAs potentially involved in heterocyst differentiation we performed an RNA-Seq analysis of cells subjected to nitrogen limitation (either at 9 or 24 hours after nitrogen removal) and analyzed the results in combination with a genome-wide set of nitrogen-regulated transcriptional start sites and a prediction of transcriptional terminators. Our analysis resulted in the definition of a transcriptional map including more than 4,000 transcripts, 65% of them in antisense orientation to other transcripts. In addition to overlapping mRNAs we identified nitrogen-regulated non-coding antisense RNAs transcribed from NtcA-dependent or HetR-dependent promoters.
Project description:Azoarcus sp. BH72 is known to express nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. NifA is the essential transcription activator of nif genes. RNA isolated from the nifA knockout mutant of strain BH72 was compared with the transcriptome of wild type under nitrogen fixing condition using a global genome wide microarray approach and the differences in the gene expression profile were monitered.
Project description:Rhizobia are soil bacteria that can enter into complex symbiotic relationships with legumes, where rhizobia induce the formation of nodules on the plant root. Inside nodules, rhizobia differentiate into nitrogen-fixing bacteroids that reduce atmospheric nitrogen into ammonia, secreting it to the plant host in exchange for carbon. During the transition from free-living bacteria to bacteroids, rhizobial metabolism undergoes major changes. To investigate the metabolism of bacteroids and contrast it with the free-living state, we quantified the proteome of unlabelled bacteroids relative to 15N-labelled free-living rhizobia. The data were used to build a core metabolic model of pea bacteroids for the strain Rhizobium leguminosarum bv. viciae 3841.
Project description:Some legume plants can establish a nitrogen-fixing symbiosis with rhizobia. Compatibilty between rhizobia and legumes is determined at species-specific level, but there are variations on the efficiency of the process determined by the capacity of the plant to select specific strains that are better partners in terms of the biological outcome. In this work we used a model system based in the coevolution of two genetic pools of common bean (Phaseolus vulgaris) with strains of R. etli that establish a more efficient interaction to study the transcriptional changes occurring in roots at an early time of the interaction.
