Regulatory RNAs in the hfq-deficient oxyphototroph Prochlorococcus sp.

• Applicant: Dr. Claudia Steglich
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2007 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 40035303

The past years have shed light on the great importance of non-coding RNAs (ncRNAs) playing important roles in the regulation of gene expression. Prochlorococcus, the organism with the most streamlined genome among oxyphotobacteria, has lost many of its protein regulators, yet the relative number of ncRNAs is comparable to other bacteria. This suggests that regulation of gene expression through ncRNAs plays a vital role in Prochlorococcus’ response to environmental cues. Recent results indicate that the class of chromosomally encoded antisense RNAs (asRNAs) might add a new level of global gene regulation. The aim of this proposal is to obtain the complete set of ncRNAs and asRNAs in Prochlorococcus in a comprehensive approach, to study the mode of action of interesting candidates and to link the results to processes in field populations, based on environmental transcriptomic analyses. Prochlorococcus is an ideal organism to investigate ncRNAs and asRNAs for the following reasons: 1.) Total genome sequences for 12 closely related Prochlorococcus strains are available allowing detailed computational predictions on ncRNAs and their possible targets. 2.) Prochlorococcus possesses the smallest genome of a free-living phototroph. Thus, the complete set of regulatory RNAs can be easily assessed. 3.) An Affymetrix high density customer microarray is available and has already been used during the last funding period for the identification of ncRNAs and asRNAs 4.) Most Prochlorococcus strains lack the otherwise widely occurring RNA chaperone. However in 2 strains Hfq is still present. Strains with and without Hfq can be studied to evaluate the role of Hfq in Prochlorcococcus.

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