Role of Hfq-binding aptamers in antisense transcripts opposite to start and stop sites of protein coding genes in E. coli

• Applicant: Professorin Dr. Renée Schroeder
• Subject Area: Biochemistry
• Term: from 2010 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 169743228

For a cell to grow in a controlled way, the synthesis of its gene products has to be tightly regulated. Until recently, studies on the regulation of gene expression were mainly focusing on regulatory proteins. However, in recent years, hundreds of regulatory RNAs have been discovered that regulate gene expression at all levels. Using genomic SELEX as an alternative approach to discover novel RNAs, we identified a large number of genomic Hfq aptamers that map to the antisense strand of protein coding genes in E. coli. These aptamers are enriched opposite to translation initiation sites and opposite to intervening sequences between genes in operons. We hypothesize that these aptamers might be involved in regulating translation or stability of their cognate mRNAs or in the differential expression of genes in polycistronic mRNAs by processing. Alternatively, Hfq aptamers might be responsible to keep the expression of antisenses transcripts low. We want to test these hypotheses by characterizing the antisense transcriptome and revealing the role of Hfq aptamers in the regulation of the E. coli transcriptome. This work might establish large antisense transcripts as an additional class of RNA molecules that control translation and/or transcriptional silencing.

• DFG Programme: Priority Programmes
• Subproject of: SPP 1258: Sensory and Regulatory RNAs in Prokaryotes
• International Connection: Austria