Small proteins in the soybean symbiont Bradyrhizobium japonicum
Justus-Liebig University Gießen (Germany), Institute for Microbiology und Molecular Biology
This project aims to uncover the repertoire of small proteins in the bacterial soybean symbiont Bradyrhizobium japonicum and to analyze the mechanisms of action of the conserved small protein RreB. In our preliminary work, we identified a conserved sORF encoding the 14 aa protein RreB, which is translated from an mRNA with an extraordinarily long Shine-Dalgarno sequence comprising 17 nt (1). In order to learn more about the role of RreB and its molecular mechanisms, we aim to study its subcellular localization and to identify its interaction partner(s). Further, we annotated more than 500 sORFs with lengths between 30 and 50 codons in the genome of B. japonicum USDA 110 (2,3). Only three of these sORFs were supported by previous proteomic analyses. Here we aim to detect small proteins in B. japonicum at a global scale. To this end two complementary approaches will be applied, peptidomics and ribosome profiling. The results will provide experimental evidence for the translation of annotated small proteins and will uncover new ones, including proteins smaller than 30 aa. This will fill in one of the last gaps in the genome annotation of B. japonicum USDA 110 and will help to improve the annotations of related symbiotic and free-living Alphaproteobacteria. We also expect that our results will contribute to the knowledge on symbiosis between rhizobia and plants.
- Hahn J, Thalmann S, Migur A, Freiherr von Boeselager R, Kubatova N, Kubareva E, Schwalbe H, Evguenieva-Hackenberg E. (2016) Conserved small mRNA with an unique, extended Shine-Dalgarno sequence. RNA Biol. 2016 Nov 11:1-11. doi: 10.1080/15476286.2016.1256534. [Epub ahead of print]
- Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E (2016) Small open reading frames, non-coding RNAs and repetitive elements in Bradyrhizobium japonicum PLoS One 11(10):e0165429. doi: 10.1371/journal.pone.0165429.
- Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg (2016) Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 17:302. doi: 10.1186/s12864-016-2602-9.