Riboregulation of photosynthesis genes in the adaptation to different growth conditions in Rhodobacter sphaeroides

• Applicant: Professorin Dr. Gabriele Klug
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 442393317

The important impact of riboregulation on the expression of photosynthesis genes in the facultative phototrophic alphaproteobacterium Rhodobacter is well documented by my previous research projects. Recent data revealed that reduced RNase E activity strongly impacts phototrophic but not chemotrophic growth, that overexpression of a single sRNA (UpsM) can abolish phototrophic growth and that RNase E also contributes to the decrease of photosynthesis mRNAs when cells leave exponential phase. This proposal will therefore address the role of riboregulation of photosynthesis genes in the adaptation to different growth conditions. To this end we will extent our existing global transcriptome data sets for wild type and some RNase mutants under different growth conditions and include further RNase mutants and a mutant lacking the RNA chaperone Hfq. All existing data sets stem from cells grown under microaerobic conditions and we will now also include aerobic and phototrophic conditions in our experiments. To understand the mechanisms underlying differential processing of sRNAs with known roles in photosynthesis gene expression under different growth conditions, we will analyze their processing and determine their half-lives in different mutant strains by Northern blots. We will establish an in vivo reporter system and also apply in vitro degradation assays to monitor the activity of RNases with a role in mRNA and sRNA processing under different growth conditions. Furthermore, we will apply co-immunoprecipitation to identify proteins that are associated with the different RNases under different growth conditions. Finally, we will elucidate the mechanisms by which the antisense RNA asPcrK affects expression of photosynthesis genes and by which the sRNA UpsM impacts phototrophic growth. These analyses will use methods that have been established in my lab in the past for analyzing the role of diverse sRNAs. We will test whether overexpression of these sRNAs affects the amount and half-lives of photosynthesis mRNAs and if so, which RNases are responsible for the altered half-lives. We want to identify direct RNA targets of UpsM and interacting proteins by the MS2 affinity purification approach, and will test whether the effect of UpsM on phototrophic growth is due to a function as Hfq sponge. We expect important new information on how RNA processing and sRNAs contribute to altered expression of photosynthesis genes when cells adapt to changing growth conditions. These results will also provide general new insights in the contribution of riboregulation to bacterial adaptation.

• DFG Programme: Research Grants