Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 6, Pages 3003-3019Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab146
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Funding
- Deutsche Forschungsgemeinschaft [Kl 561/37-1, RTG 2355]
- IZKF at the University Wurzburg [Z-6]
- Deutsche Forschungsgemeinschaft/University of Giessen
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The DUF1127 domain, present in a wide range of bacterial proteins, mediates RNA binding and affects stability, thereby modulating the bacterial transcriptome and influencing different physiological processes.
Many different protein domains are conserved among numerous species, but their function remains obscure. Proteins with DUF1127 domains number >17 000 in current databases, but a biological function has not yet been assigned to any of them. They are mostly found in alpha- and gammaproteobacteria, some of them plant and animal pathogens, symbionts or species used in industrial applications. Bioinformatic analyses revealed similarity of the DUF1127 domain of bacterial proteins to the RNA binding domain of eukaryotic Smaug proteins that are involved in RNA turnover and have a role in development from Drosophila to mammals. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in maturation of the CcsR sRNAs that are processed from the 3' UTR of the ccaF mRNA and have a role in the oxidative stress defense. CcaF1 binds to many cellular RNAs of different type, several mRNAs with a function in cysteine / methionine / sulfur metabolism. It affects the stability of the CcsR RNAs and other non-coding RNAs and mRNAs. Thus, the widely distributed DUF1127 domain can mediate RNA-binding, affect stability of its binding partners and consequently modulate the bacterial transcriptome, thereby influencing different physiological processes.
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