Project description:The samples in this series were used to analyze the transcriptome of the CtrA regulon using wild type (SB1003) and ctrA mutant (SBRM1) strains of Rhodobacter capsulatus. As well, the transcriptome of growth phase regulation in R. capsulatus SB1003 between log and stationary phases was determined.
Project description:Global transcriptome analyses at growth before and after 10 min of photooxidative stress were applied to monitor stress dependent gene expression in the alpha-proteobacterium Rhodobacter capsulatus. Transcriptome profiles of pigmented cultures with high aeration were monitored before and after the onset of singlet oxygen stress.
Project description:In this study, we achieved a global view of Cu-responsive changes in the prokaryotic model organism Rhodobacter capsulatus using label-free quantitative differential proteomics. Semi-aerobically grown cells under heterotrophic conditions in minimal medium (~ 0.3 M Cu, optimal for growth) were compared with cells grown similarly but supplemented with either 5 M Cu or with 5 mM of the Cu-chelator bathocuproine sulfonate. Mass spectrometry based bottom-up proteome analyses of unfractionated cell lysates identified with high confidence 2430 of the 3632 putative proteins encoded by the genome.
Project description:The diazotrophic bacterium Rhodobacter capsulatus synthesizes a molybdenum nitrogenase and an alternative iron-only nitrogenase, enabling growth with molecular dinitrogen as sole nitrogen source. Regulation of nitrogen fixation was analyzed by proteome profiling of wild-type and mutant strains lacking the transcriptional regulators NifA, AnfA, and MopAB.
Project description:The diazotrophic bacterium Rhodobacter capsulatus is able to synthesize two nitrogenases, a molybdenum-dependent and an alternative Mo-free iron-only nitrogenase, enabling growth with molecular dinitrogen (N2) as sole nitrogen source. The Mo response of the wild type and a mutant lacking the high-affinity molybdate transporter, ModABC, were analyzed by proteome profiling.
Project description:Nitrogenases are the only enzymes able to ‘fix’ gaseous nitrogen into bioavailable ammonia and, hence, are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited, with electron transport to the iron (Fe)-nitrogenase having hardly been investigated. Here, we characterised the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain (nifD), compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterised by monitoring diazotrophic growth and nitrogenase activity in vivo. Only deletion of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double-deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviours of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.
Project description:Transcriptomic data has been previously used to determine expression patterns in various R. capsulatus strains using custom made Affymetrix microarrays. Additional expression analyses have since been carried out to obtain preliminary data on certain wild type and mutant strains that have not been reported on. We used all current microarray expression data available and constructed an R. capsulatus gene co-expression network and performed functional analysis of identified gene modules. RNA was harvested from various wild type and mutant R. capsulatus strains grown under photoheterotrophic conditions to different growth phases. The samples were hybridized to custom made R. capsulatus Affymetrix microarrays according to manufacturers recommendations. The raw data was RMA normalized and log transformed.
Project description:Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA
