Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.

Department of Biomedical Engineering Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czech Republic

Department of Food Chemistry and Biotechnology Faculty of Chemistry Brno University of Technology Brno Czech Republic

Department of Internal Medicine Haematology and Oncology Faculty of Medicine Masaryk University Brno Czech Republic

Department of Internal Medicine Haematology and Oncology University Hospital Brno Brno Czech Republic

Institute of Life Technologies University of Applied Sciences and Arts Western Switzerland Valais Wallis Sion Switzerland

Institute of Scientific Instruments of the Czech Academy of Sciences v v i Brno Czech Republic

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